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+404: This page could not be found
For full text search please use the '?' prefix. e.g. ? Onboarding
404
This page could not be found.
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diff --git a/500/index.html b/500/index.html
new file mode 100644
index 0000000000..534967914f
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+500: Internal Server Error
For full text search please use the '?' prefix. e.g. ? Onboarding
500
Internal Server Error.
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For this we use the Dendron system as a mean to efficiently capture notes and publish them.
\n
What is this note
\n
This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.
\n
Tutorial
\n
Dendron.
\n
What is Dendron ?
\n
\n
Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
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Where to get more info on Dendron ?
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You can get more information in the Dendron system at the official website www.dendron.so
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All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.
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\n
Concrete steps to access and contribute to the DBGI Dendron
Voila ! You should now be in the COMMONS Lab Open Dendron.
\n
\n\n
Feel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at Setup
\n","note":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" 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?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null},"__N_SSG":true}
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For this we use the Dendron system as a mean to efficiently capture notes and publish them.
\n
What is this note
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This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.
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Tutorial
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Dendron.
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What is Dendron ?
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\n
Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
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Where to get more info on Dendron ?
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Concrete steps to access and contribute to the DBGI Dendron
Voila ! You should now be in the COMMONS Lab Open Dendron.
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Feel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at Setup
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null},"__N_SSG":true}
\ No newline at end of file
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For this we use the Dendron system as a mean to efficiently capture notes and publish them.
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What is this note
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This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.
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Tutorial
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Dendron.
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What is Dendron ?
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Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
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Where to get more info on Dendron ?
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Concrete steps to access and contribute to the DBGI Dendron
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Feel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at Setup
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here 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?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null},"__N_SSG":true}
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new file mode 100644
index 0000000000..80781e8582
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0eereom8dffi2c616b63hhi.json
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2023-06-26
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.26
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0rxtkzv5lbizy9q160n0oi1.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0rxtkzv5lbizy9q160n0oi1.json
new file mode 100644
index 0000000000..e4128bfc4d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0rxtkzv5lbizy9q160n0oi1.json
@@ -0,0 +1 @@
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2023-02-15
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.15
\n
Todo today
\n
\n
read some papers about Bayesian approaches for our project
\n
continue C++ lessons
\n
\n
Doing
\n
Paused
\n
Done
\n
\n
Finished learning polymorphisms in C++
\n
Finished concept of static and \"friend\" in C++
\n
Finished chapter about containers and iterators in C++
\n
Finished chapter functors C++
\n\n
\n
Notes
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0zmqus0478ehzat7p16a7sr.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0zmqus0478ehzat7p16a7sr.json
new file mode 100644
index 0000000000..3b67fe1964
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/0zmqus0478ehzat7p16a7sr.json
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/18kp75vdc5swiroffq92muf.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/18kp75vdc5swiroffq92muf.json
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+{"pageProps":{"note":{"id":"18kp75vdc5swiroffq92muf","title":"2023-09-22","desc":"","updated":1695390688649,"created":1695390645632,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.09.22","type":"note","vault":{"fsPath":"vault"},"contentHash":"b62ae623bbf51a921997ef005495293d","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.09.22","id":"18kp75vdc5swiroffq92muf","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}},{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.09.22","id":"18kp75vdc5swiroffq92muf","vaultName":"vault"},"value":"projects.commons-public.microcosmics","position":{"start":{"line":21,"column":29,"offset":348},"end":{"line":21,"column":69,"offset":388},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"projects.commons-public.microcosmics"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":24,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":25,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":27,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":34,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":36,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":38,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":40,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":43,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":44,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":47,"column":0,"depth":2}},"children":[],"parent":"n34ek93pt2py6moj7lvq9sf","data":{}},"body":"
2023-09-22
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.09.22
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
Rima found a paper on continuous flow cultivation systems.
\n
Paused
\n
Done
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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index 0000000000..6d93032aa6
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Adding a\n 📖 Comment what should be commented and pass this daily Notebook to it's Open Notebook counterpart
\n
\n
cmd+A on local Notebook (without frontmatter)
\n
cmd+o cmd+c to open new daily Open Notebook (in COMMONS)
\n
cmd+v to paste
\n
remove/comment if needed
\n
post
\n
\n
That's some lines for now and will try redirecting to Open Notebook (in MAPP, COMMONS and DBGI) as much as possible. Will not port old notes ...too much of a burden
\n
Today I learned that
\n
\n
I can output selectively a text (and not only code) depending on knitting as pdf or html. Note the results='asis' to render as text.
\n
\n
```{r, echo=FALSE, results='asis'}\nif(knitr::is_latex_output()){\n cat(\"This text will only be rendered in PDF.\")\n}\nif(knitr::is_html_output()){\n cat(\"This text will only be rendered in HTML.\")\n}\n
\n
\n- Just lost a lot of time since I wrote the MAPP activity report having in mind that I could share the Airtbale dashboard (they call this an interface) as a public link. Turns out it's not possible https://community.airtable.com/t5/other-questions/how-to-make-link-to-interface-public/td-p/81008\nAnother good reason to keep on digging in the NocoDB/Directus direction. Should have checked before.\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/1wqdwzyc4no58lzquin6r7f.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/1wqdwzyc4no58lzquin6r7f.json
new file mode 100644
index 0000000000..1bd36902cb
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/1wqdwzyc4no58lzquin6r7f.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"1wqdwzyc4no58lzquin6r7f","title":"2023-10-13","desc":"","updated":1697193774152,"created":1697192602215,"traitIds":["open-notebook-commons-rouchene"],"custom":{},"fname":"open-notebook.commons.rouchene.2023.10.13","type":"note","vault":{"fsPath":"vault"},"contentHash":"2a59066cf89a6f6662133edf04b340f1","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.rouchene.2023.10.13","id":"1wqdwzyc4no58lzquin6r7f","vaultName":"vault"},"value":"projects.commons-public.microcosmics","position":{"start":{"line":18,"column":5,"offset":312},"end":{"line":18,"column":45,"offset":352},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"projects.commons-public.microcosmics"}}],"anchors":{"this-is-rimass-commons-lab-daily-open-notebook":{"type":"header","text":"This is Rimas's COMMONS Lab daily Open Notebook.","value":"this-is-rimass-commons-lab-daily-open-notebook","line":11,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":15,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":21,"column":0,"depth":3},"daily-work-on-the-microcosmics-project":{"type":"header","text":"Daily work on the Microcosmics project","value":"daily-work-on-the-microcosmics-project","line":24,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":29,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":30,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":32,"column":0,"depth":2},"next-week":{"type":"header","text":"Next week","value":"next-week","line":39,"column":0,"depth":4},"paused":{"type":"header","text":"Paused","value":"paused","line":46,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":48,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":50,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":52,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":55,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":56,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":59,"column":0,"depth":2}},"children":[],"parent":"6ji2eab9zcj88r3x8mn8edv","data":{}},"body":"
2023-10-13
\n
This is Rimas's COMMONS Lab daily Open Notebook.
\n
Today is 2023.10.13
\n
Todo today
\n
\n
Isolation of some strains
\n
read ecoplate papers
\n\n
\n
Have a look at the COMMONS research discussion forum
Read about ecoplate.\n-isolation of strains this afternoon.
\n\n
\n
Next week
\n
\n
17-10-2023 Redrego conf
\n
18-10-2023 go to the University of Neuchâtel with PMA for the collaboration.
\n
19-10-2023 visit thun city.
\n
\n
Paused
\n
Done
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/24m2tsb9ib12egiutwxxjgp.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/24m2tsb9ib12egiutwxxjgp.json
new file mode 100644
index 0000000000..a8411a8003
--- /dev/null
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/25kuyv9rxtfx0wsayavhp6a.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/25kuyv9rxtfx0wsayavhp6a.json
new file mode 100644
index 0000000000..9b7e7511e3
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/25kuyv9rxtfx0wsayavhp6a.json
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2023-04-06
\n
This is Marco's daily open-notebook.
\n
Today is 2023.04.06
\n
Notes
\n
I think the model we have can work quite nicely with the Lotus database. I have generated some fake data and am trying to predict the parameters given to the model. It looks like it works pretty well.
\n
Also we performed Gibbs sampling for trying to predict X given μ and ϵc it seems like it is able to find X fast and accurately !
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n
Finished implementing MCMC for predicting both gamma, delta and X. Works like a charm !
\n
\n
Todo tomorrow
\n
Holiday
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2cxr093kvrg4jojokwgqrbj.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2cxr093kvrg4jojokwgqrbj.json
new file mode 100644
index 0000000000..ffc0bd6693
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2et0vj32w2vlqhsq0yhv5qa.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2et0vj32w2vlqhsq0yhv5qa.json
new file mode 100644
index 0000000000..fa4a755e27
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2et0vj32w2vlqhsq0yhv5qa.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"2et0vj32w2vlqhsq0yhv5qa","title":"Wikipathways","desc":"","updated":1646580820546,"created":1646563156580,"custom":{},"fname":"projects.commons-public.wikipathways","type":"note","vault":{"fsPath":"vault"},"contentHash":"d339c0db4353a9be4c969942d362177d","links":[{"type":"wiki","from":{"fname":"projects.commons-public.wikipathways","id":"2et0vj32w2vlqhsq0yhv5qa","vaultName":"vault"},"value":"user.49b70bc7","alias":"@49b70bc7","position":{"start":{"line":7,"column":253,"offset":413},"end":{"line":7,"column":262,"offset":422},"indent":[]},"xvault":false,"to":{"fname":"user.49b70bc7"}}],"anchors":{},"children":[],"parent":"sbfuh96mq7lxrzznz5lny1l","data":{}},"body":"
➜ pathvisio-3.3.0 sh pathvisio.sh\nProblem creating boot delegation class loader: java.lang.reflect.InaccessibleObjectException: Unable to make protected java.security.SecureClassLoader(java.lang.ClassLoader) accessible: module java.base does not \"opens java.security\" to unnamed module @49b70bc7 (Private)\nInstalling bundles that are embedded in the jar.\nDetected embedded bundle: org.apache.batik.svggen_1.7.0.v201011041433.jar\nLoading jar:file:/Applications/pathvisio-3.3.0/pathvisio.jar!/org.apache.batik.svggen_1.7.0.v201011041433.jar\n^C^C%\n➜ pathvisio-3.3.0 java --version\nopenjdk 17.0.1 2021-10-19\nOpenJDK Runtime Environment (build 17.0.1+12-39)\nOpenJDK 64-Bit Server VM (build 17.0.1+12-39, mixed mode, sharing)
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2hbho4xox7z1l9t5356q048.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2hbho4xox7z1l9t5356q048.json
new file mode 100644
index 0000000000..fa1e7d38e3
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2hbho4xox7z1l9t5356q048.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"2hbho4xox7z1l9t5356q048","title":"2023-06-02","desc":"","updated":1685688019711,"created":1685687992024,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.06.02","type":"note","vault":{"fsPath":"vault"},"contentHash":"25c89da57f6615a3a3ace69aedfefdf8","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":30,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":32,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":34,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":36,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":39,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":40,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":43,"column":0,"depth":2}},"children":[],"parent":"9y2owvmuwe3k3aj7q730usn","data":{}},"body":"
2023-06-02
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.02
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2jtc4t19xf4q6nrifhk4k9w.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2jtc4t19xf4q6nrifhk4k9w.json
new file mode 100644
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--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2jtc4t19xf4q6nrifhk4k9w.json
@@ -0,0 +1 @@
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2023-06-27
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.27
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2l0e12cc2apwv74rbsc7ma8.json
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2023-09-20
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.09.20
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2q1wc73tsex1tijg7kzjq3u.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2q1wc73tsex1tijg7kzjq3u.json
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I think the most important script for us is prepare_pseudoabsence_tables.R. It generates presence and absence tables\nof chemical compounds based on the Order. The Order could be changed to then have tables based on Family, Subfamily, Genus, etc...
\n
This will have to be discussed:
\n
\n
At what level of taxonomy do we want to work ?
\n
At what level of chemical taxonomy should we work ?
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2rvdf4t5qnx5hqjj29bojcc.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2rvdf4t5qnx5hqjj29bojcc.json
new file mode 100644
index 0000000000..d747991e7d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2rvdf4t5qnx5hqjj29bojcc.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"2rvdf4t5qnx5hqjj29bojcc","title":"Editor","desc":"","updated":1654066730457,"created":1654066694811,"custom":{},"fname":"editor","type":"note","vault":{"fsPath":"vault"},"contentHash":"4c6671584c7e9472644365ca1b660b2f","links":[],"anchors":{},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Editor
\n
Just accepted a review Editor role for Frontiers in Natural Products.\nHopefully not a mistake ...
\n
The Review Editor: The primary role of the Review Editor is to provide an expert review of Frontiers articles in a rigorous, constructive and efficient manner. Frontiers acknowledges the role of the reviewer by naming the person to the Editorial Board and by publishing the name of the Review Editor on every published paper endorsed by him or her. This practice requires Frontiers to have processes in place to transparently deal with conflicts of interest, both real and perceived.\nFrontiers Review Editors should hold, as a minimum, either a PhD with post-doctoral experience, or an equivalent degree with several additional years of academic work, or the equivalent number of years to a recognized qualification in the relevant field of research. Review Editors should have a recognized affiliation and a proven publication record in their specialty area.
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2uthwqb9xtcmgpdd821e4dr.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2uthwqb9xtcmgpdd821e4dr.json
new file mode 100644
index 0000000000..c48ee2a291
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/2uthwqb9xtcmgpdd821e4dr.json
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+{"pageProps":{"note":{"id":"2uthwqb9xtcmgpdd821e4dr","title":"2023-03-03","desc":"","updated":1677856496035,"created":1677839008087,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.03.03","type":"note","vault":{"fsPath":"vault"},"contentHash":"8e3ddb2d63359e22716312afc2d152f7","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":22,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":27,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":31,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":35,"column":0,"depth":2}},"children":[],"parent":"oxbyb3iqmrqrlvwrlt40q4m","data":{}},"body":"
2023-03-03
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.03
\n
Notes
\n
\n
After long discussion with Pierre-Marie and Daniel, we agreed on:\n
\n
2 main properties are \"molecules\" and \"species\"
\n
Adding another dimension like \"tissue\" or \"environment\" is important\n
\n
Finding which one to add is not of our concern for now.
\n
\n
\n
We could increase to how many properties as we want but what is the scientific relevance of doing that ? For now it would make sense just to keep the tissue
\n
\n
\n
\n
Todo today
\n
\n
Continue on generalization of the model, find a way to increase properties to an infinite number of dimensions
\n
Correct nomenclature and keep the same for the rest of the model.
\n
Try to write Hastings ratio to update our parameters
\n
\n
Doing
\n
\n
continue on the \"upper\" part of the model
\n
\n
Done
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..90e2340660
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/36354ldtt6g7yq3uvrjykle.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/403.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/403.json
new file mode 100644
index 0000000000..536b677c9b
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Dendron (the tool used to generate this site) lets authors selective publish content. You will see this page whenever you click on a link to an unpublished page
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/43p60vv8btyhaclugl93jok.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/43p60vv8btyhaclugl93jok.json
new file mode 100644
index 0000000000..6fc9517485
--- /dev/null
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answer back editor regarding delay for the viewpoint synopsis\nDraft at viewpoint.communication.emails.npr-editor (Private)\nIndicated end of July for the submission of the synopsis\nSent 2023-06-24 19:09
\n
\n
Friday 23 June 2023
\n
Initial invitation email
\n
\n
Dear Pierre-Marie,
\n
I hope you are doing well,
\n
Since a number of years, I have been on the editorial board of Natural Product Reports.\nI saw the nice website of your group (https://www.unifr.ch/bio/en/groups/allard/), and this made me think: might you be interested in writing a Viewpoint (together with any relevant co-authors) on open science in natural products research?
\n
If you are enthusiastic, the next step would be to prepare a synopsis (see attachments for instructions), which I would then circulate among the editorial board for suggestions and approval.
\n
I am looking forward to hearing what you think!
\n
\n
Attachements at \nAttachements at
\n
Yesterday answered to the NPR editor.
\n
\n
Many thanks for your email and invitation.
\n
I am pretty much interested in your suggestion as I believe writing and proposing ressources and perspectives on the topic of Open Science is of interest in most disciplines.\nI would be happy to propose such Viewpoint for the field of NP research.
\n
I have already some possible coauthors in mind and have discussed with some.\nThey are willing to participate but everyone is (like always nowadays) somehow underwater.\nWhat would be the delays (if any) to hand over this Viewpoint ?
\n
Second point would it be possible to have it published in Open Access (it would indeed be ironical to have such article paywalled)
\n
\n
His answer
\n
\n
Great to hear back from you. And fantastic to hear that you are enthusiastic about contributing something on this topic.
\n
Yes, submitting the synopsis somewhat later is no problem. When do you think you can send it in?
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4ffq6a88aj7ngobavx9ca4c.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4ffq6a88aj7ngobavx9ca4c.json
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4ffq6a88aj7ngobavx9ca4c.json
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2023-05-02
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.05.02
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4l5nn3xi9lpn1v2bgh8p72b.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4l5nn3xi9lpn1v2bgh8p72b.json
new file mode 100644
index 0000000000..73c3900728
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4l5nn3xi9lpn1v2bgh8p72b.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4s3eb3inrva89wubys0vzw9.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4s3eb3inrva89wubys0vzw9.json
new file mode 100644
index 0000000000..2419ba0b73
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/4s3eb3inrva89wubys0vzw9.json
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+{"pageProps":{"note":{"id":"4s3eb3inrva89wubys0vzw9","title":"2023-04-24","desc":"","updated":1682352023335,"created":1682347069433,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.04.24","type":"note","vault":{"fsPath":"vault"},"contentHash":"fb8af8821857a66ee556251f8091e960","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":16,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":19,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":22,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":28,"column":0,"depth":2}},"children":[],"parent":"kzei5nishi0yuojckqly29b","data":{}},"body":"
2023-04-24
\n
This is Marco's daily open-notebook.
\n
Today is 2023.04.24
\n
Notes
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n
Discussion with Daniel about new approach. For now we still keep the old model but we adapt the variance covariance matrix to reduce it's size.
\n
\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/500e30vbwe1wc5nky5wvoiw.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/500e30vbwe1wc5nky5wvoiw.json
new file mode 100644
index 0000000000..cf6aa428ba
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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2023-02-10
\n
This is PMAS's COMMONS Lab daily open-notebook.
\n
Today is 2023.02.10
\n
Todo today
\n
Have a look at the XXXX discussion forum
\n
- https://github.com/orgs/XXXXX/discussions\n
\n
\n
\n
Doing
\n
\n
refactoring traits and templates so as to have the possibility to generate daily open-notebooks notes across all public and private Dendrons.\nLet's see if the fact to have a common open-notebook.hierarchy cross Dendron workspace doesn't leads to conflicts.
\n
\n
Apparently this implies to copy individual Dendron's Note traits to the Multiworkspace Dendron but shortcuts can be shared.
\n
Paused
\n
Done
\n
Notes
\n
\n
Checked the GNPS + metabolite annotation with Stephanie this morning.
\n
\n
It would be good to have a list of Anacardiaceae metabolites.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/58rff0p6b74lecqkualu899.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/58rff0p6b74lecqkualu899.json
new file mode 100644
index 0000000000..372aeeebc4
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/58rff0p6b74lecqkualu899.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"58rff0p6b74lecqkualu899","title":"2023-04-25","desc":"","updated":1682496353277,"created":1682432647503,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.04.25","type":"note","vault":{"fsPath":"vault"},"contentHash":"01dd6fabf55e7add7f338d6571cced4a","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"changes-to-implement-in-the-model":{"type":"header","text":"Changes to implement in the model","value":"changes-to-implement-in-the-model","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":23,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":26,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":29,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":33,"column":0,"depth":2}},"children":[],"parent":"kzei5nishi0yuojckqly29b","data":{}},"body":"
2023-04-25
\n
This is Marco's daily open-notebook.
\n
Today is 2023.04.25
\n
Changes to implement in the model
\n
We made a mistake in the variance covariance matrix. In fact, we should have a product between the values of the covariances matrices and not a sum. For example, if I take two species that have 0 correlation and one molecule. Does having that molecule in one of the species give me any additional information about the presence of that molecule in the other species ? Other than the average presence μ NO we can't have any other information !
\n
We thus have cov(ϵc,ϵc′)=∏t∏f=1Ftσtf(τt(c),τt(c′)αtf)
\n
Furthermore, in order to reduce the variance covariance matrix, we first assume that a lot of molecules and a lot of species share no correlation. This, in theory, would allow us to split the data before creating the cov matrix of molecules and the cov matrix of species. This would imply to assume that some molecules and some species share 0 covariance.
\n
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/59ftsVxFXXM9bB43vfKwK.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/59ftsVxFXXM9bB43vfKwK.json
new file mode 100644
index 0000000000..33c9a89ce9
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/59ftsVxFXXM9bB43vfKwK.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/68pld3tjh6e232hyilw4vxm.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/68pld3tjh6e232hyilw4vxm.json
new file mode 100644
index 0000000000..e5af1fcf18
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/68pld3tjh6e232hyilw4vxm.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"68pld3tjh6e232hyilw4vxm","title":"2022-08-14","desc":"","updated":1660460868456,"created":1660456873108,"traitIds":["daily-notebook-pma"],"custom":{},"fname":"daily.notebook.pma.2022.08.14","type":"note","vault":{"fsPath":"vault"},"contentHash":"2ddd268aba2c3bee752bd702c19bf6b9","links":[],"anchors":{"this-is-pmas-daily-notebook":{"type":"header","text":"This is PMA's daily notebook.","value":"this-is-pmas-daily-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":20,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":26,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":32,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":77,"column":0,"depth":2},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":84,"column":0,"depth":2}},"children":[],"parent":"bts1ikiboznfyfw10536hh0","data":{}},"body":"
2022-08-14
\n
This is PMA's daily notebook.
\n
Today is 2022.08.14
\n
Todo today
\n
\n\n\n\n
\n
Doing
\n
\n\n\n\n
\n
Done
\n
\n\n\n\n
\n
Notes
\n
\n
This morning I am wanting to use a docker image which is supposed to run on localhost:8080\nHowver this one is allready used\nsee\n
\n
\n
I need to find which process is using this and stop it
\n
Solution one. Use findanyfile and search for \"It works!\" string\nNot working
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6jflwqoiwlv9jyrjbjq0xkp.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6jflwqoiwlv9jyrjbjq0xkp.json
new file mode 100644
index 0000000000..bcf6e78fc9
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6jflwqoiwlv9jyrjbjq0xkp.json
@@ -0,0 +1 @@
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2023-05-08
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.05.08
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ji2eab9zcj88r3x8mn8edv.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ji2eab9zcj88r3x8mn8edv.json
new file mode 100644
index 0000000000..224cba3012
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ji2eab9zcj88r3x8mn8edv.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ooxuf27zzf3grb14o18qf2.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ooxuf27zzf3grb14o18qf2.json
new file mode 100644
index 0000000000..a27e8e84bf
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6ooxuf27zzf3grb14o18qf2.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"6ooxuf27zzf3grb14o18qf2","title":"Awk","desc":"","updated":1687874851232,"created":1687874706004,"custom":{},"fname":"awk","type":"note","vault":{"fsPath":"vault"},"contentHash":"e1bfeaeb4c0a89bedab50efc8f65cd9f","links":[],"anchors":{"sirius-outputs-formatting":{"type":"header","text":"Sirius outputs formatting","value":"sirius-outputs-formatting","line":8,"column":0,"depth":1}},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Awk
\n
Sirius outputs formatting
\n
These commands require to have awk and csvcut installed on your system.
\n
The code processes a file named canopus_compound_summary.tsv. It searches for a field called \"id\" in the file's header. If found, it splits the values in that field by underscores and adds a new column called \"feature_id\". It then modifies the header by appending \"_canopus\" to each field name and prints the modified header. After that, it extracts specific columns and saves the extracted data. Finally, the extracted data is formatted as tab-delimited and saved in a file called canopus_compound_summary_id.tsv.
The code processes a file named compound_identifications.tsv. It searches for a field called \"id\" in the file's header. If found, it splits the values in that field by underscores and adds a new column called \"feature_id\". It then modifies the header by appending \"_sirius\" to each field name and prints the modified header. After that, it extracts specific columns and saves the extracted data. Finally, the extracted data is formatted as tab-delimited and saved in a file called compound_identifications_id.tsv.
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6y7lyl389amsc5m9n4ixg6f.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6y7lyl389amsc5m9n4ixg6f.json
new file mode 100644
index 0000000000..e1f8ecb912
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/6y7lyl389amsc5m9n4ixg6f.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"fname":"open-notebook.commons.sguetchueng","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254246,"created":1697541254246,"id":"6y7lyl389amsc5m9n4ixg6f","desc":"","links":[],"anchors":{},"children":["chv7fzfor3tr4ajck3nhgw8"],"parent":"ne6ca7ufq0o7dqjc8q2ilnk","data":{},"title":"Sguetchueng"},"body":"
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7dxoqlg3l911jll5cnusrvs.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7dxoqlg3l911jll5cnusrvs.json
new file mode 100644
index 0000000000..a165905ef2
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7dxoqlg3l911jll5cnusrvs.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"7dxoqlg3l911jll5cnusrvs","title":"2023-03-16","desc":"","updated":1678968993661,"created":1678968961730,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.03.16","type":"note","vault":{"fsPath":"vault"},"contentHash":"93c3c11f31142203793533500ccb0a8a","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":16,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":19,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":22,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":26,"column":0,"depth":2}},"children":[],"parent":"oxbyb3iqmrqrlvwrlt40q4m","data":{}},"body":"
2023-03-16
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.16
\n
Notes
\n
Todo today
\n
\n
continue learning statools and try some things
\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7ecl420o90am8q0dszrh19e.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7ecl420o90am8q0dszrh19e.json
new file mode 100644
index 0000000000..e861df93b7
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7ecl420o90am8q0dszrh19e.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"7ecl420o90am8q0dszrh19e","title":"Cookie Cutter","desc":"","updated":1646416439555,"created":1646409467048,"custom":{},"fname":"reproducibility.templates.cookie-cutter","type":"note","vault":{"fsPath":"vault"},"contentHash":"5429b35816b8b17ae8caa9ce8f20df7f","links":[],"anchors":{},"children":[],"parent":"flc2uvmagtzu8d89n88cz0j","data":{}},"body":"
Cookie Cutter
\n
Tired of having non consistent folder for MAPP Metabolomics reports.\nLooking into cookie cutter (for data science) as a possible template to start with and have more consistency across these repos.
Stop at 1:04:00 and workinh here /Users/pma/Dropbox/git_repos/mapp-metabolomics-unit/cookie_cut_project
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7jn0di38ou7vesl580yxwl5.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7jn0di38ou7vesl580yxwl5.json
new file mode 100644
index 0000000000..6fe1b95e11
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/7jn0di38ou7vesl580yxwl5.json
@@ -0,0 +1 @@
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📖 Comment what should be commented and pass this daily Notebook to it's Open Notebook counterpart
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
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2023-07-08
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.08
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..e45b2542b3
--- /dev/null
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9i4brqx31bc3bmth1dtsdc9.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9i4brqx31bc3bmth1dtsdc9.json
new file mode 100644
index 0000000000..439cdb9361
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9i4brqx31bc3bmth1dtsdc9.json
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+{"pageProps":{"note":{"id":"9i4brqx31bc3bmth1dtsdc9","title":"Exchanged","desc":"","updated":1688798801817,"created":1688797053899,"custom":{},"fname":"viewpoint.communication.emails.exchanged","type":"note","vault":{"fsPath":"vault"},"contentHash":"60d3355fbb78011e671bf8b7c4ac3e22","links":[],"anchors":{"recap-of-exchanged-ideas-and-comments-in-the-emails":{"type":"header","text":"Recap of exchanged ideas and comments in the emails","value":"recap-of-exchanged-ideas-and-comments-in-the-emails","line":9,"column":0,"depth":1}},"children":[],"parent":"xk2ymgnu5t1i8gdb7lyos4j","data":{}},"body":"
Exchanged
\n
Recap of exchanged ideas and comments in the emails
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9nu26axhshlukejhh7yin28.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9nu26axhshlukejhh7yin28.json
new file mode 100644
index 0000000000..954ec2c516
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9nu26axhshlukejhh7yin28.json
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+{"pageProps":{"note":{"fname":"projects.commons-public.microcosmics.metabolomics","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254227,"created":1697541254227,"id":"9nu26axhshlukejhh7yin28","desc":"","links":[],"anchors":{},"children":["habtsdf8nwmm3oowinqhi6h"],"parent":"0zmqus0478ehzat7p16a7sr","data":{},"title":"Metabolomics"},"body":"
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9oj9c91gnuxqd9yq3izn4re.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9oj9c91gnuxqd9yq3izn4re.json
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@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"9oj9c91gnuxqd9yq3izn4re","title":"2023-04-23","desc":"","updated":1682250967244,"created":1682248090700,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.04.23","type":"note","vault":{"fsPath":"vault"},"contentHash":"8208bcf84af68d9df1f991d927518223","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":58,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":60,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":62,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":64,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":67,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":68,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":71,"column":0,"depth":2}},"children":[],"parent":"itinl4oosihdr0r1gc1t929","data":{}},"body":"
2023-04-23
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.04.23
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
Beautiful is better than ugly.\nExplicit is better than implicit.\nSimple is better than complex.\nComplex is better than complicated.\nFlat is better than nested.\nSparse is better than dense.\nReadability counts.\nSpecial cases aren't special enough to break the rules.\nAlthough practicality beats purity.\nErrors should never pass silently.\nUnless explicitly silenced.\nIn the face of ambiguity, refuse the temptation to guess.\nThere should be one-- and preferably only one --obvious way to do it.\nAlthough that way may not be obvious at first unless you're Dutch.\nNow is better than never.\nAlthough never is often better than right now.\nIf the implementation is hard to explain, it's a bad idea.\nIf the implementation is easy to explain, it may be a good idea.\nNamespaces are one honking great idea -- let's do more of those!
\n
Paused
\n
Done
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9qsbp81ci31s52m5xb3sf3t.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9qsbp81ci31s52m5xb3sf3t.json
new file mode 100644
index 0000000000..75515cc2d9
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9qsbp81ci31s52m5xb3sf3t.json
@@ -0,0 +1 @@
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2023-04-27
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.04.27
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9rdwrsd8asjnhvcvnhy2fcn.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9rdwrsd8asjnhvcvnhy2fcn.json
new file mode 100644
index 0000000000..8bf00f3ff0
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..7bfe76e1cd
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9sd95l7fisv0jth1val07w2.json
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2023-07-04
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.04
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9y2owvmuwe3k3aj7q730usn.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9y2owvmuwe3k3aj7q730usn.json
new file mode 100644
index 0000000000..c51c76cabe
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/9y2owvmuwe3k3aj7q730usn.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/B0vi9qnffoq1jF6SVDZ4e.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/B0vi9qnffoq1jF6SVDZ4e.json
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@@ -0,0 +1 @@
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Create_item
\n
[TOC]
\n
Manual addition of a documented structure-organism pair to Wikidata
\n
Select a documented structure-organism pair
\n
Throughout this demonstration, we are going to use the following example:
Check for the presence of your compound in Wikidata
\n
Using the compound's InChIKey (i.e. QOVGHDRCAGYGEB-FFZYJECLSA-N for trigocherrin A), run a SPARQL query to check if your compound is present in Wikidata or not:
\n
SELECT?item?itemLabelWHERE{\n VALUES?classes{\n wd:Q11173# chemical compound\n wd:Q59199015# group of stereoisomers\n wd:Q79529# chemical substance\n wd:Q17339814# group of chemical substances\n wd:Q47154513# structural class of chemical compounds\n }\n ?itemwdt:P31?classes.# instance of\n ?itemwdt:P235'QOVGHDRCAGYGEB-FFZYJECLSA-N'\n SERVICEwikibase:label{bd:serviceParamwikibase:language\"[AUTO_LANGUAGE],en\".}\n}\n
\n
Try this query. You can adapt it by replacing the InChIKey with the one for your compound.
First, if you do not have a Wikidata account already, it is advisable that you create one via https://www.wikidata.org/wiki/Special:CreateAccount. While an account is not strictly required for manual edits, having one will be useful if you want to contribute more than once, and it helps in getting your contributions recognized. Note that Wikidata accounts are integrated with accounts across the Wikimedia ecosystem, so if you already have an account on, say, any Wikipedia or on Wikispecies, then you can use the same credentials on Wikidata.
Click publish to save your changes and make them public.
\n
Since you created a new item about an instance of a chemical compound, the user interface will automatically propose to you a set of additional statements commonly found on items about chemical compounds.
\n
\n
You can then go on and fill these in.
\n
Here, we start with the InChIKey.\nNote the little flag which will automatically tell you if you have some problems with the recently created statements.
\n
\n
Here, Wikidata tells us that if we add an InChiKey, we will need to also add an InChI. Logical, but good to have a reminder !
\n
Let's go ahead and add the InChI string.
\n
Likewise, the addition of an isomeric SMILES string will require us to add a Canonical SMILES.
\n
Note that you might have to copy and paste the SMILES string from PubChem to a plain text editor and then back to Wikidata because of some formatting issues when copy pasting directly from PubChem.
Just click on Add a new statement and type in the first letters of the property you want to add:
\n
\n
Again, type in the first letters of the taxon, and if the organism is present, it will autocomplete. Here is how this looks like for Trigonostemon cherrieri:
\n
\n
Click publish to save your changes and make them public.
\n
If your target taxon is not yet present on Wikidata and you are sure you have a valid taxon name that is spelled correctly, then you can go to https://www.wikidata.org/wiki/Special:NewItem, as described in the Add your data manually to Wikidata section. For items about taxa, the instance of statement should have a value taxon (i.e. Q16521). As for chemical compounds, the user interface will then suggest to you further statements to add. For taxa, these include taxon name, parent taxon and taxon rank.
\n
Add the reference documenting the structure-organism pair
\n
Finally, since we report documented structure-organisms pairs, we need to add the reference for this newly created compound found in taxon relationship.\nThis happens on the item about the compound, just below the found in taxon statement. Click on the 0 references link and then on add reference:
Now, type in the first letters or word of the scientific publication documenting the natural product occurence, autocompletion happens again. Note that multiple publications might have the same title, and that there could be minor differences in punctuation or special characters between the information you and Wikidata have about the same reference. If you are not sure whether your target reference is already in Wikidata, you can use its DOI to check, as outlined in the Check whether your target reference is already on Wikidata section.
\n
\n
Click publish to save your changes and make them public.
\n
\n
Check whether your target reference is already on Wikidata
\n
If you are not sure whether your target reference is already in Wikidata, you can use its DOI to check. For our DOI 10.1021/ol2030907, the URL https://scholia.toolforge.org/doi/10.1021/ol2030907 will lead you to a Scholia page about this publication: https://scholia.toolforge.org/work/Q83059010. Scholia visualizes information from Wikidata, so if it has an entry for your target reference, then so does Wikidata, and both of them will use the same identifier (in this case Q83059010). If you prefer to resolve your DOI to Wikidata directly, you can do so by using the uppercase-normalized DOI in the following URL pattern: https://hub.toolforge.org/P356:10.1021/OL2030907, which will lead you to the respective Wikidata page, in this case Q83059010.
\n
If you think that no Wikidata entry exists for your target reference, you can use the DOI in the URL pattern https://sourcemd.toolforge.org/index_old.php?id=10.1021/ol2030907&doit=Check+source, which will trigger a check with both Crossref and Wikidata, and if no Wikidata entry can be found, the metadata from Crossref will be fetched and presented to you for creating the respective Wikidata item semi-automatically. Using such semi-automated workflows does require and account that is a minimum number of days old and has made a minimum number of edits on Wikidata.
You have added your first documented structure-organism relationship to Wikidata and made a valuable contribution to the community.\nYou can add further statements, e.g. molecular formula, or SPLASH code for linking to spectral data.
You can run a SPARQL query and check that everything went smoothly by modifying the InChiKey line in the following SPARQL query:
\n
SELECT?item?itemLabel?taxonLabel?artLabelWHERE{\n VALUES?classes{\n wd:Q11173# chemical compound\n wd:Q59199015# group of stereoisomers\n wd:Q79529# chemical substance\n wd:Q17339814# group of chemical substances\n wd:Q47154513# structural class of chemical compounds\n }\n ?itemwdt:P31?classes.# instance of\n ?itemwdt:P235'QOVGHDRCAGYGEB-FFZYJECLSA-N'# InChiKey\n {\n ?itemp:P1582?stmt.# natural product of taxon\n ?stmtps:P1582?taxon.# natural product of taxon\n OPTIONAL{\n ?stmtprov:wasDerivedFrom?ref. \n ?refpr:P248?art.# stated in\n }\n }\n UNION\n {\n ?itemp:P703?stmt.# found in taxon\n ?stmtps:P703?taxon.# found in taxon\n OPTIONAL{\n ?stmtprov:wasDerivedFrom?ref.\n ?refpr:P248?art.# stated in\n }\n }\n SERVICEwikibase:label{bd:serviceParamwikibase:language\"[AUTO_LANGUAGE],en\".}\n}\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/C25Rc7ww2GhogRkrCBCNe.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/C25Rc7ww2GhogRkrCBCNe.json
new file mode 100644
index 0000000000..7a08fb5572
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/C25Rc7ww2GhogRkrCBCNe.json
@@ -0,0 +1 @@
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In order to have metabolites for a genus and below
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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Mismall
\n
This is a placeholder to test xvaults
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/Ykcls825joDD8WIqXdtCg.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/Ykcls825joDD8WIqXdtCg.json
new file mode 100644
index 0000000000..556ddc8627
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/Ykcls825joDD8WIqXdtCg.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"Ykcls825joDD8WIqXdtCg","title":"Docker Singularity","desc":"","updated":1678183849488,"created":1634195008546,"custom":{},"fname":"courses.docker-singularity","type":"note","vault":{"fsPath":"vault"},"contentHash":"3fcf737e3e423eb777dec176771bc305","links":[],"anchors":{"concepts":{"type":"header","text":"Concepts","value":"concepts","line":33,"column":0,"depth":1},"image":{"type":"header","text":"Image","value":"image","line":35,"column":0,"depth":2},"container":{"type":"header","text":"Container","value":"container","line":44,"column":0,"depth":2}},"children":["k2ZyWqz1dvbZP4gWGXlzf"],"parent":"jldFUSJGjDf1mFH8c2yUI","data":{}},"body":"
Please make sure to have read the page with the technical requirements previous to the course.
\n
Slack workspace:\nWe will use a Slack workspace to work collaboratively. Please make sure to have connected to this space before the course starts.
\n
Google Doc:\nWe have also created a gdoc to simplify the exchanges of information with you during the lectures: Link Google doc. We suggest that you keep this document open during the course.
read-only\nstored on longer term\ncan be used as a base
\n
Container
\n
based on the image\nshort lived\nusually for minor adjustements
\n
(Apparently the delay in the suggestion mode should be enough to mange the annoying suggestions.\nAnother option would be to set up the acceptation key to somethinh other than automatic.)
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/a190edwty8eeyo3sfuqcq4n.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/a190edwty8eeyo3sfuqcq4n.json
new file mode 100644
index 0000000000..0cb64d8d74
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/a190edwty8eeyo3sfuqcq4n.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"a190edwty8eeyo3sfuqcq4n","title":"2023-02-14","desc":"","updated":1676454294688,"created":1676364390201,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.02.14","type":"note","vault":{"fsPath":"vault"},"contentHash":"164f39ab317d63f378d7a477686fd253","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":13,"column":0,"depth":2},"":{"type":"header","text":"","value":"","line":17,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":18,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":20,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":23,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":25,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":34,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":41,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":43,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":44,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":45,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":48,"column":0,"depth":2}},"children":[],"parent":"f7kju6sk6wivpqr1onnfy4u","data":{}},"body":"
2023-02-14
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.14
\n
Todo today
\n
\n
still publish PDF online because images and DAGs don't work.
\n
change DAG to split MS data and lotus
\n
\n
\n
\n
Doing
\n
\n
Trying to create multiple DAG and see which one is correct for our model.
\n
\n
Paused
\n
Done
\n
\n
Used pandoc to convert latex file into markdown and then passed it into
\n
\n
Discussion with Pierre-Marie about the structure of MS and what could be used to implement the model.
\n
\n
We shouldn't forget that our model will likely not be on a 3D molecular level but a 2D since mass spec is not able to make the difference between enantiomers.
\n
Notes
\n
Sirius and ISDB = info to molecular level\nCANOPUS info to NPC (NP classifier class)
\n
\n
ysm is the probability of having a molecule in a species
\n
μm is the average presence of one molecule across all species.
\n
ysm is then the average presence across all species plus an error ϵ. And that is why we assume that error is normally distributed across the mean μ.
\n
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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02
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/aqe35lqv5khojyw2y5eottk.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/aqe35lqv5khojyw2y5eottk.json
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2023-09-28
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.09.28
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/b4d9mlfhjpghpnhvvdgtwq5.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/b4d9mlfhjpghpnhvvdgtwq5.json
new file mode 100644
index 0000000000..ac06c716b3
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/b4d9mlfhjpghpnhvvdgtwq5.json
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-check why I can commit on github\n-make a little plan of what I would like to do\n-work with Pierre-Marie to fix the issue on git hub\n-work with Edouard on inaturalist\n-sample extraction first batch 12 samples
\n
Notes
\n
i have to run visualcode as administrator\nthere is a possibility to write notes even after the date
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..3e847b9f8e
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/bi8ogqo6nes6wlj9j2do4oz.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/bi8ogqo6nes6wlj9j2do4oz.json
new file mode 100644
index 0000000000..bf53d95ebe
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/bkkax85vpq62949ouqqjq6g.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/bkkax85vpq62949ouqqjq6g.json
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Draft
\n
*Guidelines for submitting a synopsis to Natural Product Reports
\n
NPR articles are designed to give an interesting insight into the topic, focussing on the key developments that have shaped a field rather than giving a very comprehensive overview of all results. Authors are encouraged to include their own perspective on developments, trends and future directions.\nBefore commissioning articles for NPR we ask that authors provide a brief synopsis. This is circulated to members of the editorial board for comment.
Please include the following information in your synopsis:
\n
*1. A proposed title for the work
\n
Open Science in Natural Products Research
\n
*2. Authors and affiliations (including co-authors if known)
\n
\n
ACS: Ana Claudia Sima, SIB Swiss Institute of Bioinformatics, Amphipôle, 1015 Lausanne, Switzerland, ORCID: 0000-0003-3213-4495
\n
AR: Adriano Rutz: Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093, Switzerland. ORCID: 0000-0003-0443-9902
\n
DM: Daniel Mietchen: Leibniz Institute for Freshwater Ecology and Inland Fisheries, Müggelseedamm 310,\n12587 Berlin. ORCID: 0000-0001-9488-1870
\n
ELS: Emma L. Schymanski: Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg. ORCID: 0000-0001-6868-8145
\n
EW: Egon Willighagen: Department of Bioinformatics - BiGCaT, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands. ORCID:0000-0001-7542-0286
\n
JB: Jonathan Bisson: Collaborative Drug Discovery, Burlingame, CA, USA ORCID: 0000-0003-1640-9989
\n
JMN: Jean-Marc Nuzillard: Université de Reims Champagne-Ardenne, CNRS, ICMR, Reims, France. ORCID: 0000-0002-5120-2556
\n
PMA: Pierre-Marie Allard: Department of Biology, University of Fribourg, Ch. du Musée 10, 1700 Fribourg, Switzerland. ORCID: 0000-0003-3389-2191
\n
PMR: Peter Murray Rust
\n
TK: Tobias Kühn
\n
\n
Donat Agosti : to invite. Great experience regarding the advancement of taxon / taxonomic treatments handling.
\n
This part (current credit attribution and authorship methods could also be discussed and guidelines proposed ?\nI have done some bibliography on this for another project. What looked like the fairest way and simplest is the one proposed by \"The first author takes it all? Solutions for crediting authors more visibly, transparently, and free of bias\" https://bpspsychub.onlinelibrary.wiley.com/doi/10.1111/bjso.12569 and others. Basically alphabetical ordering of the authors + two clear CRediT tables (one by tasks done, one by authors) looks random enough (should be stated explicitely) and explain who has been doing what. The idea is to break the first/last author monopoly which is not the best way to credit authors contrib. A colleague told me that we shouldn't / coulnt do this with PhD, MSc students because they NEED their first author paper. Im happy to hear your thought here. This small app makes it easy to implement such tables. (In a paper like this one it's maybe overkill as their is not much more than writing involved ...) They also suggest everyone should let their email and be corresponding authors.\nYou put me wherever you want, as long as it helps the people in fields where author positions matter.
\n
See this vbiewpoint as suggestion to ediotrs.\nFor ex. adoption of the CREDIT for authors in NP journals
\n
*3. A suggested length of the article – this should be the number of printed journal pages
\n
Max. 8 printed pages
\n
*4. The time span of the literature you intend to cover
\n
From antiquity to nowadays.
\n
*5. A brief description of the review and topic to be covered, including:
\n
This synopsis aims to provide an overview of the emerging field of open science in natural products research, highlighting its significance, key principles, and potential impact on the field. Natural products have long been a valuable source of compounds with diverse biological activities, contributing to the development of novel drugs, foods and dyes; and form the basis of the traditional medicine used by the vast majority of the world's population. However, the traditionally closed and proprietary nature of natural products research has limited and still hinders the accessibility, reproducibility, and collaboration within the scientific community. The concept of open science promotes transparency, accessibility, and collaboration through the unrestricted sharing of research outputs, data, and methodologies. In this review, we will explore the various aspects of open science in the context of natural products research, including open access publishing, open data, open source software, citizen science initiatives, and collaborative networks. We will discuss the benefits, challenges, and potential solutions associated with adopting an open approach in natural products chemistry, emphasizing the potential for accelerating scientific discovery, fostering innovation, and promoting global collaboration in this vital field. Additionally, we will present novel guidelines for publishing and documenting natural products occurrences, with the aim of proposing standardized practices that could be readily adopted by researchers and publishers in the field. By establishing clear and comprehensive guidelines, we seek to enhance the FAIRness (Findability, Accessibility, Interoperability and Reusability) of natural products research, ultimately fostering a more open and collaborative scientific ecosystem.\n
\n
Implications for the wider scientific community:
\n
The adoption of open science in natural products research promotes transparency, collaboration, and accessibility. It enhances the reproducibility and reliability of research, accelerates knowledge dissemination, and facilitates the development of NP's applications. It also fosters inclusivity and global collaboration within the scientific community, ultimately advancing the field and benefiting society as a whole. However the transition to open research requires sustained efforts and resources, and these are best mobilized when the benefits of open science are clearly identified by the researchers. Currently, funding agencies are progressively enforcing research outputs, processes and methodologies to be open, making such global transition inevitable in the end. In addition, open science helps people from less privileged places to both learn from and join in on advanced research, breaking down the usual barriers. For individuals outside the institutions of science and industry, it makes complex knowledge easier to access, understand and use, leading to better decisions and creative solutions for problems in their own communities and the wider world.
\n
Communities the article will appeal to:
\n
natural products chemists, pharmacologists, medicinal chemists, organic chemists, biochemists, ecologists, cheminformaticians and researchers interested in open science and description of the global chemodiversity.\nIt is also relevant to professionals in academia, industry, regulatory agencies, and those involved in the dissemination of knowledge, including librarians, publishers, and policymakers.
\n
We therefore aim to address an entire ecosystem, from Knowledge Producers to Knowledge Disseminators in Natural Products Research, as we strongly believe that communities need to act together to improve the health of the whole natural products ecosystem, and that Open Science provides the necessary path and opportunity for strengthening this collaboration in going forward.
\n
*6. Suggested section headings
\n
1. Overview of Natural Products Research from antiquity to nowadays\n2. Emergence and current landscape of Open Natural Products Research\n3. Key Principles of Open Science in the Context of Natural Products Research\n4. The Significance of Open Science in Advancing Natural Products Research\n5. Proposed solutions for Publishing and Documenting Natural Products\n
\n
Here, we will notably propose a semantically-enriched version of the current viewpoint, a semantically-enriched version of a typical NPR hot-off-the-press (e.g. https://pubs.rsc.org/en/content/articlelanding/2023/np/d3np90029k) and propose to editors a simpler and easy to adopt mechanism for the enhancement of Natural Products Research dissemination (a CSV file to be shared in Supplementary Information, or as a Zenodo repository associated to the published paper).
\n
*7. A brief list of key references, noting any other reviews which have been published in the area.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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index 0000000000..faa4c867ce
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..9fd46691fd
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cfty88t52bo6eiiymlozz35.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cfty88t52bo6eiiymlozz35.json
new file mode 100644
index 0000000000..b347e8d042
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Gadget
\n\n\n\n\ntrigocherrin A - Wikidata\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..99f6ca5c61
--- /dev/null
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/clbok7e7y7fr5w39vcq5svp.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/clbok7e7y7fr5w39vcq5svp.json
new file mode 100644
index 0000000000..076271a1b9
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/clbok7e7y7fr5w39vcq5svp.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"clbok7e7y7fr5w39vcq5svp","title":"2023-07-28","desc":"","updated":1690523628362,"created":1690523628362,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.07.28","type":"note","vault":{"fsPath":"vault"},"contentHash":"e93dcd11c7a823c27f8bf0fcd54e26d7","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.07.28","id":"clbok7e7y7fr5w39vcq5svp","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":24,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":25,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":27,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":29,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":31,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":33,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":35,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":38,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":39,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":42,"column":0,"depth":2}},"children":[],"parent":"p9uxp04cqx16vq7f9tvg8m8","data":{}},"body":"
2023-07-28
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.28
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cljk03e4kdxplqegnigounp.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cljk03e4kdxplqegnigounp.json
new file mode 100644
index 0000000000..bc6f247327
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cljk03e4kdxplqegnigounp.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"cljk03e4kdxplqegnigounp","title":"Meetings","desc":"","updated":1695715243888,"created":1695714710167,"custom":{},"fname":"projects.commons-public.microcosmics.meetings","type":"note","vault":{"fsPath":"vault"},"contentHash":"58c4173b2b0c7d9ca47ab4043d894431","links":[],"anchors":{"tuesday-26-september-2023":{"type":"header","text":"Tuesday 26 September 2023","value":"tuesday-26-september-2023","line":9,"column":0,"depth":1}},"children":[],"parent":"0zmqus0478ehzat7p16a7sr","data":{}},"body":"
Meetings
\n
Tuesday 26 September 2023
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..95a1c5e0ec
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/cm7lxhcj1gc5cubsyzd3811.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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index 0000000000..56c98c5963
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Standards don't send you money now, they send you money later
\n
G. Grieve
\n
\n
Q: Hi Katrin. Thanks for the talk ! On one slide you mentioned the importance of efforts regarding integration of omics data within the SPHN KG.\nAre these future tasks or are they currently undertaken ? I am particularly interested to know wether they are concrete things done on the integration of metabolomics data.\nWhat are the challenges here according to you ?
\n
National Data streams.
\n
Integration of genomics + other omics\nTwo of them integrate metabolomics data Partners on the data stream. Curated with an expert team in Zurich
have the 1600 pf dataset ind files uploaded on Zenodo
\n
Think about a structure for individual \"capsule\" per profile.\nIt would include all required metdata, raw files and resulting individual RDF\nCould be uploaded to Zenop using their API.\nEach profiled sample wpould thus benefit from its individual doi
\n
\n
Q: what wouldn't fit in such a capsule ?
\n
Todo tomorrow, another day ... or never !
\n
Mechanism to copy assets
\n
When transfering daily notes from notebook.xxxx. to open-notebook.xxxx the assets stay in the orignal vault where they were pasted. This leads to broken link.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..7eefb2e08b
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/d30ba4veecrymlt6pq60dh1.json
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Rouchene
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This is Rimas's COMMONS Lab daily Open Notebook.
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Todo today
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/dgak1qyfpecqt8r3iyqcleh.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/dgak1qyfpecqt8r3iyqcleh.json
new file mode 100644
index 0000000000..fd5fcd74c4
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/dgak1qyfpecqt8r3iyqcleh.json
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Have the equivalent of open-notebook.commons.pmallard for mapp
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Today I learned that
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See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e090r2p38a55v6gv4uuezue.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e090r2p38a55v6gv4uuezue.json
new file mode 100644
index 0000000000..85fdb6dfe4
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e090r2p38a55v6gv4uuezue.json
@@ -0,0 +1 @@
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removed samples from the freeze dyer\nsample dbgi_1105 need to be redry. the cap used on tube was not appropiate for the freeze dyer.\ncncentrate Methanol samples of batch 1
\n
Notes
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e4ul30admmxm9ilxfq275cq.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e4ul30admmxm9ilxfq275cq.json
new file mode 100644
index 0000000000..16eb9d094a
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/e4ul30admmxm9ilxfq275cq.json
@@ -0,0 +1 @@
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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section","value":"composition-of-culture-media-prepared-solution-supplemented-and-chemicals-used-in-the-experimental-section","line":202,"column":0,"depth":3},"you-have-to-do-tomorrow":{"type":"header","text":"you have to do tomorrow","value":"you-have-to-do-tomorrow","line":224,"column":0,"depth":3},"rima-note-12-10-23":{"type":"header","text":"Rima note 12-10-23","value":"rima-note-12-10-23","line":232,"column":0,"depth":3},"i-learned-how-to-share-image-with-dendronn":{"type":"header","text":"I learned how to share image with Dendronn","value":"i-learned-how-to-share-image-with-dendronn","line":235,"column":0,"depth":1},"done-1":{"type":"header","text":"Done","value":"done-1","line":239,"column":0,"depth":3},"doing-1":{"type":"header","text":"Doing","value":"doing-1","line":243,"column":0,"depth":3},"ask-pma":{"type":"header","text":"ASk PMA","value":"ask-pma","line":248,"column":0,"depth":3},"to-do-tomorow":{"type":"header","text":"to do 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2023-10-11
\n
This is Rimas's COMMONS Lab daily Open Notebook.
\n
Today is 2023.10.11
\n
Todo today
\n
Getting started with Dandron with PMA
\n
Have a look at the COMMONS research discussion forum
I carried out the first sampling at the botanical garden. I took a horizon of 3- 12 cm.\nSee pic [[]]\n[[]]\n[[]]\n\n\n
\n
10-10-2023 Check the inoculated plates.
\n
Look pic [[]]\n[[]]\n[[]]\n[[]]
\n
\n\n\n
\n
\n
Doing
\n
Working on the eerimental design off the roject.\nCollecting infos and pdf and woring at Experimental Design.
\n
Paused
\n
Done
\n
How to write note in Dendron and to sync with public commons web.
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n
using ctrl+O+N i can creat a dialy note
\n
ctrl+s to save my modification
\n
ctrl+L search or create note
\n
share picture link (Private)\nctrl+shift+P show pallette
\n
\n
Setting up of the Microcosmics project
\n
Literature
\n
Useful before setting up the microcosmis system
\n
Microcosm incubation
\n
12-h photoperiod: Columbia View orchard soil was passed through a 4-mm sieve and 100 g samples were placed into 487 mL microcosms (glass jars). Jar lids were perforated to make a 1 cm diameter hole into which a rubber septum was inserted. The experiment consisted of two treatments; ASD amended with rice bran (RB) and a no-carbon input ASD control (ASD-NA), seven time points; day 0, 1, 2, 3, 7, 11, and 15, with four samples per treatment at each incubation duration point. In total, across all treatments and time points, 56 samples analyzed. For the purposes of this study, RB soil amendment treatment was not included as pathogen suppression (e.g., F. oxysporum f. sp. fragariae) was not realized under such conditions (Figure 1). In addition, RB soil incorporation does not yield an anaerobic environment (Mazzola et al., 2018), nor result in amplification of target microbial populations commonly associated with ASD-induced disease suppression, such as Clostridium spp. For the ASD treatment, 1.57 g of RB (equivalent to 20 Mg per ha per 15 cm depth in the field) was homogeneously mixed into soil. Estimated nutrient concentration of RB was C = 47.8%, N = 2.49%, P = 1.53%, K = 1.60%, S = 0.18%, C:N ratio = 19:1, pH = 6.2 (Soiltest Farm Consultants, Inc., Moses Lake, WA, United States). For both treatments, 25 mL of distilled water was added to saturate the soil pore spaces. The headspace volume over the microcosms was 409 mL. Jars were incubated in an environmental growth chamber for 15 days at 24/18°C with 12-h photoperiod. Photosynthetically active radiation (PAR, 400–700 nm) just above the jars was 226 μmol m–2 sec–2. Immediately after initiating the experiment, headspace volatiles were extracted, and a representative soil sample was collected using a #3 cork borer (7 cores from each microcosm). Soil samples were placed in a chilled sample cup, followed by immediate immersion in liquid nitrogen and stored at −80°C. This procedure was followed for soil sampling at all incubation duration points. Frozen soil cores were cryogenically milled to a fine powder and stored again at −80°C before use for metabolite analysis. For day 0 and day 1 time points, headspace O2 and CO2 composition was analyzed every 4 h and once for the remaining incubation duration points as described below (https://www.frontiersin.org/articles/10.3389/fmicb.2019.02365/full).
\n
LC/MS analysis ( soil metabolomics)
\n
Extraction of the metabolome and LC-MS analysis:\nMethod 1. Extracellular metabolites were extracted from 2 g of wet soil from each sample (with five technical replicates) using 10 ml of deionized water. The samples were shaken on a mechanical shaker for 12 hours at 4°C, then centrifuged at 2,500 x g for 15 minutes at 4°C, and finally filtered through 0.2 µm polyethersulfone membrane filters (Pall Corporation, New York, NY, USA). Polar metabolites were completely dried using a rapid vacuum concentrator, then chemically derivatized and analyzed by gas chromatography-mass spectrometry (GC-MS) (https://www.mdpi.com/2076-2607/10/8/1653].
\n
Method 2. Biocrust soil water samples (1.5 mL) were lyophilized and resuspended in methanol (200 μL) containing internal standards (2–10 μg/mL) and filtered through 96-well Millipore filter plates (0.2 μm PVDF) by centrifuging at 1500 × g for 2 min. Samples were analyzed using normal-phase LC/MS with a ZIC-pHILIC column (150 × 2.1 mm, 3.5 μm 200 Å, Merck Sequant, Darmstadt, Germany) using an Agilent 1290 series UHPLC (Agilent Technologies, Santa Clara, California, USA)(https://www.nature.com/articles/s41467-017-02356-9).
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Method 3. (Soil non-targeted metabolomic detection and analysis) Twelve rhizosphere soil samples were sent to Majorbio (Shanghai, China) on dry ice for metabolite extraction, detection, and analysis. In detail, 1,000-mg soil aliquot of each sample was homogenized with 1,000 µL methanol/water (4:1, v/v) solution, including 0.02 mg/mL internal standard (L-2-chlorophenylamine acid) for 6 min at −10 °C and 50 kHz using a Geno-grinder 2,000 (SPEX, Metuchen, NJ, USA) and spun down for 30 min at 5 °C and 40 kHz. After resting for 30 min at −20 °C, each material was centrifuged at 13,000 g (relative centrifugal force) for 15 min at 4 °C, then the supernatant was transferred and concentrated by a Termovap Sample Concentrator (DC-24, Anpel Laboratory Technologies, Shanghai, China). The dry residue was derivatized by adding 50 µL acetonitrile/water (1:1), homogenized for 30 s at 5 °C and 40 kHz, and centrifuged at 13,000 g (relative centrifugal force) for 10 min at 4 °C. Finally, the supernatant was subjected to LC-tandem MS (MS/MS) analysis; 20 µL supernatant of each sample was mixed for the quality control sample.\nThe UHPLC-Triple TOF system (AB Sciex, Foster City, CA, USA) equipped with an ACQUITY UPLC HSS T3 (100 mm × 2.1 mm i.d., 1.8 µm; Waters, Milford, CT, USA) was applied to chromatographic separating the metabolites with two mobile phases, phase A (95% water and 5% acetonitrile (with 0.1% formic acid)) and phase B (5% water (with 0.1% formic acid), 47.5% acetonitrile, and 47.5% isopropanol). The whole system was integrated to a quadrupole time-of-flight mass spectrometer (Triple TOFTM 5600th; AB Sciex, Foster City, CA, USA) equipped with an electrospray ionization source and operated in positive and negative modes doi: 10.7717/peerj.13254.
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Method 4. The 45 collected soil samples, and 5 blank samples containing no soil, were lyophilized on an Edwards Super Modulyo freeze-drier (SciQuip Ltd., Shropshire, UK) for 7 d. Subsequently, these were ground in a Retsch MM200 stainless steel ball mill (Retsch GmbH, Haan, Germany) at a frequency of 20 Hz to aid recovery of metabolites from the microbial biomass (Fiehn et al., 2002; Wang et al., 2015). The samples were then stored in individual sterile glass vials at −80 °C to minimize changes in metabolites (Wellerdiek et al., 2009). The soils were extracted using 3:3:2 (v/v/v) acetonitrile-isopropanol-water, vortexed for 15 s, shaken at 4 °C for 5 min, centrifuged at 1400 rpm for 2 min, and dried using a CentriVap Benchtop Centrifugal Concentrator (Labconco Corp., Kansas City, MO) (Barupal et al., 2019; Fu et al., 2019). Non-targeted primary metabolism analysis was performed using a Gerstel Automated Linear Exchange-Cold Injection System (ALEX-CIS) with Agilent gas chromatograph (GC) and Leco Pegasus IV Time Of Flight (TOF) MS at the UC Davis West Coast Metabolomics Facility using the method of Fiehn (2016). Briefly, 0.5 μl of each sample was injected onto a Rtx-5Sil MS capillary column (30 m length × 0.25 m i.d with 10 m integrated guard column; 0.25 μm 95% dimethylsiloxane/5% diphenylpolysiloxane coating; Restek Corp., Bellefonte, PA). Using a He mobile phase, the GC thermal programme was 50 °C for 1 min, ramped to 330 °C at 20 °C min−1 and finally held at 330 °C for 5 min. Upon elution, samples were injected into a Pegasus IV GC-time of flight mass spectrometer (Leco Corp., St Joseph, MI), using mass resolution of 17 spectra s−1, from 80 to 500 Da, at −70 eV ionization energy and 1800 V detector voltage with a 230 °C transfer line and 250 °C ion source (https://www.sciencedirect.com/science/article/pii/S0038071720300559).\nMethod 5 (3 methods in the same paper): Soil Sample Extractions for NMR and MS Analyses\nExtraction in DMSO\nAntarctic soil (2 g) was suspended in 10 mL of DMSO, sonicated at 37 kHz, pulse, 100 pw, 30 min, 30–60 °C (Elmasonic P 30 H, Elma Schmidbauer GmbH, Singen, Germany). Each sample was centrifuged (Beckman Avanti J-20 Centrifuge, Beckman Coulter, Indianapolis, IN, USA) at 20,000× g for 15 min, 4 °C. The supernatant was collected and freeze-dried (Christ Alpha 1-2 LD plus, Martin Christ Gefriertrocknungsanlagen GmbH, Osterode am Harz, Germany). The extraction yield was calculated for each sample. Lyophilized samples were stored at −20 °C.\nExtraction in H2O/CH3OH 1:1\nAntarctic soil (2 g) was suspended in 10 mL of MilliQ water/CH3OH 1:1 with 50 µL NaN3 0.3 M to obtain NaN3 1.5 mM (0.01%), sonicated and centrifuged as described above. The supernatant was collected and CH3OH evaporated under reduced pressure at 40 °C (Heidolph Rotary Evaporator, Laborota 4000, Heidolph Instruments GmbH & Co. KG, Schwabach, Germany). The water phase was transferred in flask and freeze-dried as above. The extraction yield was calculated for each sample. Lyophilized samples were stored at −20 °C.\nExtraction in H2O/CH3CN 7:3\nAntarctic soil (2 g) was suspended in 10 mL of MilliQ water/CH3CN 7:3 with 50 µL NaN3 0.3 M to obtain NaN3 1.5 mM (0.01%) sonicated at 37 kHz, pulse, 100 pw, 60 min, 30–60 °C, and centrifuged as described above. The extraction was repeated with 10 mL of fresh extraction solution. The supernatants were transferred in a flask and freeze-dried as above. The extraction yield was calculated for each sample. Lyophilized samples were stored at −20 °C (https://www.mdpi.com/1422-0067/24/15/12340).\nMethod 5 (+ ammonium bicarbonate) 5 g of lyophilized soil were placed in a 25 ml centrifuge tube equipped with a Teflon-lined screw cap and 4 ml of 0.25 M aqueous ammonium bicarbonate, 10 ml methanol, and 5 ml chloroform containing the internal standards for NLFA and PLFA analysis (trinonadecanoin glyceride, Nu-Chek Prep, Inc., Elysian, MN, USA; 19:0 phosphatidylcholine, Avanti Polar Lipids, Alabaster, AL), were added. The contents of the centrifuge tubes were then sonicated 10 min in a water bath sonicator at room temperature, incubated at room temperature with end-over-end mixing for 2 h, and centrifuged 10 min at 1710 G. The liquid phase was transferred to a 30 ml test tube with a Teflon-lined screw cap, 5 ml each of water and chloroform were added, and the sample mixed by vigorous shaking. After centrifuging for 10 min at 1710 G, 2 layers were formed. The top layer (aqueous phase) contained the water-soluble metabolites while the bottom layer (organic phase) contained the lipids. Each phase was transferred into a separate test tube and evaporated in vacuo using a centrifugal evaporator. The organic phase was evaporated to dryness for NLFA and PLFA analyses while the aqueous phase was evaporated to approximately one-quarter of the original volume for metabolomic analysis. Samples were stored at −80 °C until further processing (https://www.sciencedirect.com/science/article/pii/S0929139318309958?casa_token=Ke9s59BsPbMAAAAA:m0W7-gJGUad-_iMOcfnUumQW_JYGiiW9exCDR7bVKgGh0JTUPbzVJq_X2I94sHOyuGtfys5Ftw).\nMethod 7. methanol–chloroform–water method [DOI: 10.1002/etc.2418].
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Determination of Soil Microbial Biodiversity
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Through amplicon sequencing (Illumina MiSeq):\nThe diversity of soil bacteria and fungi was analyzed through amplicon sequencing (Illumina MiSeq). A total of 10 g of frozen soil samples were cooled using liquid nitrogen and ground using a mortar and pestle. Soil DNA (n = 435) was extracted using a DNA Isolation Kit (Powersoil, MoBio Laboratories, Carlsbad, CA, USA). A portion of the bacterial 16S and eukaryotic 18S rRNA genes were sequenced using the 515F/806R and Euk1391f/EukBr primer sets, respectively (https://doi.org/10.1038/s41396-021-00906-0.
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Relevance of biolog plates
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ECOPLATE : The EcoPlate contains 31 carbon sources that are useful for community analysis. These 31 carbon sources are repeated 3 times to give the scientist more replicates of the data. Communities of microorganisms will give a characteristic reaction pattern called a metabolic fingerprint. From a single EcoPlate, these fingerprint reaction patterns rapidly and easily characterize the community (https://sci-hub.se/https://doi.org/10.1016/j.apsoil.2015.06.007).\nL’Eco-plate est une microplaque de 96 puits dans lesquels se trouvent un substrat carboné et un colorant. Cette plaque doit être inoculée par une solution environnementale contenant une communauté microbienne provenant notamment du sol. Elle regroupe 3 réplicas d’une série de 31 substrats carbonés et un contrôle négatif (eau). Ces substrats représentent 6 classes différentes de composés carbonés : amines/amides, hydrates de carbone, polymères de carbone, acides carboxyliques, acides aminés, phosphates organiques (Preston-Mafham et al., 2002) (Annexe 1). Ils représentent les sources de carbone les plus retrouvés dans l’environnement terrestre, la majorité d’entre eux étant issus de matière végétale (exemple : D-Xylose). Ce choix de substrats a été déterminé ainsi pour apporter des informations suffisantes et pertinentes dans le cas d’étude des populations bactériennes de l’environnement. Par ailleurs, chaque puits contient aussi un sel de tétrazolium qui sert d’indicateur coloré positif. En effet ce sel va jouer le rôle d’accepteurs d’électron artificiel dans la chaine respiratoire des bactéries. Ainsi, lorsque les bactéries métabolisent le substrat, ce sel est réduit de manière irréversible en un composé violet insoluble : le formazan (Tachon et al., 2009). La production de formazan est alors quantifiée par mesure de la densité optique à 590 nm (OD590nm). L’OD590nm est alors proportionnelle à la consommation du substrat (chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://www.secure.mg/sites/default/files/2019-01/Ecoplate-Version-Courte.pdf).\nThe limitations: Le principal reproche fait à l’Eco-Plate est que ses conditions d’incubations ne sont pas celles du sol. Il se peut que ce métabolisme ne puisse pas s’exprimer dans le contexte naturel. De plus, l’apport d’une seule source de carbone à la fois induit en effet une pression de sélection vis-à-vis du substrat en faveur de celles ayant un métabolisme rapide supportant une forte concentration en un seul nutriment (Garland et al., 1997 ; Preston-Mafham et al., 2002 ; Muñiz et al., 2014). Le CLPP pourrait donc ne refléter que la capacité d’une communauté bactérienne à supporter les conditions de la plaque : des bactéries capables d’intégrer ce sel de tétrazolium dans leur chaine respiratoire, qu’elles soient cultivables ou non, mais ayant un métabolisme rapide et aérobie, (Winding et al., 1997 ; Preston-Mafham et al., 2002). D’un puits à l’autre, la diversité n’est donc pas la même et elle diminue par rapport à la communauté inoculée (Garland et al., 1997). De plus, alors qu’ils représentent des organismes très actifs dans les sols, les champignons ne sont pas représentés dans les Eco-Plates car ce sel de tétrazolium n’est pas adapté à leur métabolisme. Il existe cependant la plaque Biolog FF adaptée pour les étudier (Preston-Mafham et al., 2002 (chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/https://www.secure.mg/sites/default/files/2019-01/Ecoplate-Version-Courte.pdf)
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isolation of soil microrganisms
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Isolation of Fungal Strains from Soil Samples: Solid potato dextrose agar (PDA) media were used for the isolation and identification of fungal strains. The inoculum prepared from soil samples was spread on PDA medium, and incubation was carried out at 28 ± 2°C for 5 to 7 days. After incubation, the morphology of the colonies was recorded to identify the specific fungus collected in each sample (ref) [https://www.mdpi.com/2304-8158/10/6/1280].\nFor bacteria: Starch casien agar(https://www.nature.com/articles/202928a0).\nWe prepared a mineral solution composed of 2 g/L (NH4)2SO4, 4 g/L KH2PO4, 6 g/L Na2HPO4, 0.05 g/L CaCl.2H2O,\n0.2 g/L MgSO4.7H2O, and 0.01 g/L FeSO4.7H2O (https://link.springer.com/article/10.1007/s11270-016-2789-z).
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Ecoplate
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According to So et al., the EcoPlates™ test, especially when applied to soil, can be challenging to replicate and standardize due to the lack of detailed procedures and protocols. The main issues with this technique primarily concern soil preparation, bacterial inoculum densities, and the correct definition of the reference value (blank) when calculating diversity indices. Based on our previous research in agricultural soils, we propose a standardized and precise step-by-step method for assessing the functional diversity of a soil bacterial community using Biolog® EcoPlates (https://www.mdpi.com/2076-3417/9/19/4035).
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We prepared 1:100 dilutions from 10 g subsamples, inoculated the EcoPlate with these diluted subsamples, incubated the plates at in situ temperature, and made measurements on Days 0, 1, 3, 5, 7, 10, and 14. The first step was to inoculate samples into an EcoPlate, either as aqueous samples or after suspension. The utilization of each carbon source during incubation was coupled to the conversion of triphenyl tetrazolium chloride to triphenyl formazan (TPF), so that carbon utilization could be quantified by the color density of TPF in each well using the optical density at 590 nm with a microplate reader (iMark; Bio-Rad Laboratories). Detailed information on EcoPlate, including the 31 carbon substrates, is available at https://www.biolog.com/wp-content/uploads/2020/05/00A-012-rD-EcoPlate-IFU.pdf (last accessed on November 9, 2021). [Correction added on 3 March 2022, after first online publication: information about the microplate reader was amended in the preceding paragraph]
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Due to its small volume (100 μl/well), the community size can be less than 10,000 individuals/well, which is a nonnegligible source of stochasticity in the initial species composition among the 96 wells in a plate. This could result in variation in color density among identical substrates within a plate (Zhou et al., 2013). To reduce the stochastic effect, three repeated sets of 31 different response wells were conducted for each plot (https://esj-journals.onlinelibrary.wiley.com/doi/full/10.1111/1440-1703.12293).
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Protocol
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Measure 10 g of the soil sample.
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Add 10 ml of distilled water and gently shake the flask.\"
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Inoculate the ecoplate with 100 µL for each well.\"
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Incubate plates at 37°C.\"
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Read at 590 nm on days 0, 1, 3, 5, 7, 10, and 14.
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Experimental design of microcosmics project
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Materials and Methods
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Preliminary microcosm optimization step
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_Preparation of Microcosms\n_We do not have data on the lab's microcosm resistance duration. Therefore, we have created three different batches of 200 grams of soil. The first batch (control) consists of soil sterilized in an autoclave at 121 °C for one hour. The second microcosm, called the natural microcosm, underwent no modifications. The last type is the microcosm enriched with a mineral solution to maintain the basic metabolism of the microcosm and promote the growth of slow-growing microorganisms, as shown in the experimental plan in Figure 1. Each of these three types of microcosms will be replicated four times, giving us a total of twelve microcosms for measurements after 1 week, 15 days, 21 days, and 30 days. All microcosms were incubated at 28 °C. All components used for the microcosms were sterilized in an autoclave for 30 minutes at 121 C.
In the first step, we optimized the soil metabolome extraction protocol. To achieve this, we extracted 5 grams of soil using five extraction methods: M1, M2, M3, M4, and M5. Subsequently, the mixtures were allowed to rest for 2 hours, after which they underwent sonication at 37 kHz with a 100-pulse wave for 30 minutes at a temperature range of 30-60°C. Following this, the samples were centrifuged at 20,000× g for 15 minutes at 4°C. The supernatants were collected and stored at -20°C for further analysis.\nMethod 1: 100% methanol.\nMethod 2: 80%,20%, 0.01% (Methanol/ H2O/Formic acid).\nMethod 3: 100% DMSO.\nMethod 4: 4ml of ammonium bicarbonate + 10 ml methanol+ 5ml of chloroform.\nMethod 5: 4ml of ammonium bicarbonate + 10 ml ethyl acetate.\nAll the extractions have a final volume of 15 ml with 5 g of soil.\nAdditionally, 0.5 grams of the sample were diluted in 4 milliliters of sterile distilled water and vigorously shaken. A volume of 100 μL of the diluted sample was inoculated onto various culture media, including SCA supplemented with antimicrobials (nalidixic acid, cycloheximide, and nystatin), PDA, nutrient agar, and A4. The plates were incubated at 28°C, except for those inoculated on nutrient agar, which were incubated at 37°C.
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comments after applying
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the five methods are not coonslusive - the search for other methods is essential. Weak profiles
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- Others etraction methods: \n
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The 45 collected soil samples, and 5 blank samples containing no\nsoil, were lyophilized on an Edwards Super Modulyo freeze-drier (SciQuip Ltd., Shropshire, UK) for 7 d. Subsequently, these were ground in a Retsch MM200 stainless steel ball mill (Retsch GmbH, Haan, Germany)\nat a frequency of 20 Hz to aid recovery of metabolites from the microbial biomass (Fiehn et al., 2002; Wang et al., 2015). The samples were then stored in individual sterile glass vials at -80°C to minimize changes in metabolites (Wellerdiek et al., 2009). The soils were extracted using 3:3:2 (v/v/v) acetonitrile-isopropanol-water, vortexed for 15 s, shakenat 4° C for 5 min, centrifuged at 1400 rpm for 2 min, and dried using a CentriVap Benchtop Centrifugal Concentrator (Labconco Corp., Kansas City, MO) (Barupal et al., 2019; Fu et al., 2019). Non-targeted primary metabolism analysis was performed using a Gerstel Automated Linear Exchange-Cold Injection System (ALEX-CIS) with Agilent gas chromatograph (GC) and Leco Pegasus IV Time Of Flight (TOF) MS at the UC Davis West Coast Metabolomics Facility using the method of Fiehn (2016). Briefly, 0.5 μl of each sample was injected onto a Rtx-5Sil MS capillary column (30 m length ° 0.25 m i.d with 10 m integrated guard column; 0.25 μm 95% dimethylsiloxane/5% diphenylpolysiloxane coating; Restek Corp., Bellefonte, PA). Using a He mobile phase, the GC thermal programme was 50 °C for 1 min, ramped to 330°C at 20° C min 1 and finally held at 330 °C for 5 min. Upon elution, samples were injected into a Pegasus IV GC-time of flight mass spectrometer (Leco Corp., St Joseph, MI), using mass resolution of 17 spectra s1 , from 80 to 500 Da, at 70 eV ionization energy and 1800 V detector voltage with a 230 °C transfer line and 250°C ion source https://doi.org/10.1016/j.soilbio.2020.107758 (Private).
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-- _Protocol steps_\n - Lyophilization of the samples for 7 days.\n -Grinding in a stainless steel ball mill Retsch at a frequency of 20 Hz.\n -The samples were then stored in individual sterile glass vials at -80°C.\n -The soils were extracted using a 3:3:2 (v/v/v) acetonitrile-isopropanol-water solution. The mixture was vortexed for 15 seconds, shaken at 4°C for 5 minutes, and then centrifuged at 1400 rpm for 2 minutes. Finally, the samples were dried using a CentriVap Benchtop CentriVap.\n
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Prior to use, all glassware was acid-washed (5% HCl, > 24 h) to remove chemical residues, rinsed in HPLC-grade water three times, and subsequently dry heat sterilised (150 °C, 2.5 h) (Jain et al., 2020). All equipment used to process the soil (e.g., tweezers and spatulas) were thoroughly cleaned both before and between samples with deionised water and 70% industrial methylated spirit (IMS) to prevent cross-contamination. Nutrients in the concentrations described in section 2.2 were added by pipette in 1 ml of HPLC-plus grade water (Sigma-Aldrich, Munich, Germany) evenly distributed across the surface of 10 g fresh weight of soil in 240 ml polypropylene sample containers (Snap-Seal®; Corning, NY, USA). This type of container was used to ensure even coverage of the soil surface with the nutrient solution (soil depth ca. 10 mm). Five independent soil replicates (n = 5) were set up per treatment. Samples were subsequently incubated as described in Section 2.2. At the end of the incubation period, the soil samples were immediately transferred to 20 ml glass vials and fumigated with ethanol-free chloroform for 24 h to lyse microbial cells, to increase metabolite yield (Swenson et al., 2015) and limit microbial processing of metabolites, using the method of Vance et al. (1987). After fumigation, samples were immediately frozen (−80 °C) to quench any residual metabolic and enzymatic activity (Wellerdiek et al., 2009). From this point onwards, all samples were stored at −80 °C, unless otherwise stated and while being processed (i.e. out of the freezer), samples were kept on ice (4 °C). Lyophilisation of samples (>24 h) was then performed using a Modulyo Freeze Dryer (ThermoFisher Corp, Waltham, MA) equipped with an RV vacuum pump (Edwards Ltd., Crawley, UK). Samples were then mechanically ground using a Retsch MM200 stainless steel ball mill (Retsch GmbH, Haan, Germany) for 60 s at a frequency of 20 Hz to aid in cell lysis and metabolite recovery and to increase sample homogeneity (Wang et al., 2015; Withers et al., 2020). The ball mill was cleaned thoroughly between samples with HPLC-grade water followed by 70% IMS, to avoid contamination.\nThe following extraction method is based on the hybridised methods of Swenson et al. (2015) and Fiehn et al. (2008). Briefly, we used the extraction method from Swenson et al. (2015) and the solvent makeup (3:3:2) from Fiehn et al. (2008), to ensure broad metabolite coverage, with the recovery of both polar and non-polar metabolite classes. Further, the weight of soil extracted was increased in order to maximise the volume of supernatant available for lyophilisation and subsequent analysis. A pre-experiment was used to compare the efficiency of the metabolite extraction method proposed here to that of the Swenson et al. (2015) method (the results are summarised in supplementary information Section S1).
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Upon soil extraction, 6 g of each fumigated, lyophilised, ground soil sample was weighed into a 35 ml glass centrifuge tube (Kimax®; DWK Life Sciences, Stoke-on-Trent, UK), to which 24 ml of pre-cooled (−20 °C) acetonitrile (MeCN)/isopropyl alcohol (IPA)/HPLC-plus grade water (H2O) (3:3:2 v/v/v) extractant was added, using a glass pipette. Samples were then horizontally shaken on ice (4 °C) at a frequency of 200 Hz for 1 h, and then centrifuged at 3320×g for 15 min (Swenson et al., 2015). Supernatants were then transferred, using glass pipettes, into 20 ml glass vials and stored at −20 °C (to ensure metabolic activity was quenched but the supernatant was not frozen). Samples were left unfiltered due to the potential of contamination from dissolution of contaminants from the filter paper and plastic housing. The supernatant was lyophilised in 2 ml glass vials using a Modulyo Freeze Dryer with RV pump attached to a SpeedVac vacuum concentrator (Savant; ThermoFisher Corp.). The vials were periodically topped up with the supernatant, taking note of the quantity added (∼15 ml total) and lyophilised to complete dryness. Samples were then shipped on dry ice (−78.5 °C) to Metabolon Inc. (Morrisville, North Carolina, USA) for untargeted LC-MS metabolomic analysis. Upon analysis, samples were dissolved in methanol:water (4:1 v/v) and subjected to the standard Metabolon sample preparation procedure. Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS) analysis parameters, bioinformatics, compound ID and data curation are summarised in Supplementary information Section S2.
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Composition of culture media, prepared solution supplemented, and chemicals used in the experimental section
-praparation of blancks for LC-MS analysis\n-boites checked\nToday I observed the appearance of the first actinomycete spores on SCA + ATB plates and a fungus on PDA medium.
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Doing
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literature
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ASk PMA
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organise a doodle with the soil team
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to do tomorow
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-check plates.
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isolation of same strains with diferent aspects in particular actino and fungi.
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Today is 13-10-2023
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To do
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Isolation of some strains
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read ecoplat papers
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Done
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I have isolated actinomycetes on SCA, named S1-S8 (B1, B2 or B3 means they come from the same isolation plate).\nI've isolated 2 fungi (ch1,Ch2) of different aspect on PDA.
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Program next week
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LC-MS analysis of the first extraction 9-10-2023.
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after the fisrt LC-MS, second extractin with the best prtocol.
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17-10-2023 Redrego conf.
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19-10-2023.\n-18-10-2023 going to the University of Neuchâtel with PMA for collaboration.
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Visit Thun city.
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Today 16-10-2023
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To do
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LC-MS run with PMA
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check plates
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Done
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We submitted the samples containing the blanks from RO_01_07_01 to RO_01_07_10 for LC-MS analysis. However, the profiles obtained are inconclusive. Therefore, the search for other extraction protocols is essential.
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I have also isolated two other strains of fungi.
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Édouard showed me his DBGI extraction method.
\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ejXhjipWcHZkFh8dQkNad.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ejXhjipWcHZkFh8dQkNad.json
new file mode 100644
index 0000000000..972189ef0d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ejXhjipWcHZkFh8dQkNad.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"ejXhjipWcHZkFh8dQkNad","title":"Assane","desc":"","updated":1631858586929,"created":1631858240713,"custom":{},"fname":"projects.commons-public.wikidata.assane","type":"note","vault":{"fsPath":"vault"},"contentHash":"7d33dd7481bee953aaa0a70a6d8e1749","links":[],"anchors":{},"children":[],"parent":"FWyOwAt9PiD3jHX3Kb275","data":{}},"body":"
Assane
\n
Batch creation of short url for WD SPARQL queries.
Bjonnh: faut juste urlencoder l'url de ta query (donc double encodage!)
\n
Bjonnh: python fait ça facile
\n
Bjonnh: et tu mets ça dans le paramètre url
\n
Bjonnh: tout ça tu peux le faire en python avec requests et urlencode. Left as an exercise for you ;)
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/etro8bpif29iqqr8fcrrl9a.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/etro8bpif29iqqr8fcrrl9a.json
new file mode 100644
index 0000000000..d08a08af88
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/etro8bpif29iqqr8fcrrl9a.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"etro8bpif29iqqr8fcrrl9a","title":"2023-02-07","desc":"","updated":1675758866048,"created":1675758746461,"traitIds":["open-notebook-sguetchueng"],"custom":{},"fname":"open-notebook.commons.sguetchueng.2023.02.07","type":"note","vault":{"fsPath":"vault"},"contentHash":"63baecda890e9678a07a126be8396d0a","links":[],"anchors":{"this-is-stephanies-daily-open-notebook":{"type":"header","text":"This is Stephanie's daily open-notebook.","value":"this-is-stephanies-daily-open-notebook","line":9,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":13,"column":0,"depth":2},"have-a-look-at-the-dbgi-discussion-forum":{"type":"header","text":"Have a look at the DBGI discussion forum","value":"have-a-look-at-the-dbgi-discussion-forum","line":18,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":20,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":21,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":23,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":25,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":27,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":29,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":31,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":33,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":34,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":35,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":38,"column":0,"depth":2}},"children":[],"parent":"36354ldtt6g7yq3uvrjykle","data":{}},"body":"
2023-02-07
\n
This is Stephanie's daily open-notebook.
\n
Today is 2023.02.07
\n
Todo today
\n
fresh plant material collection and processing, 4 species from Anacardiaceae\ndocumentation on GNPS\nread two papers\nwork on the malaria project
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..d97c90408d
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/f4i5k5mtdzqddttvgvbe7uc.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/f4i5k5mtdzqddttvgvbe7uc.json
new file mode 100644
index 0000000000..8f15d278aa
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/f7kju6sk6wivpqr1onnfy4u.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/f7kju6sk6wivpqr1onnfy4u.json
new file mode 100644
index 0000000000..66f2e86381
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/f7kju6sk6wivpqr1onnfy4u.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fda86oc8rtm4cof9hbkwwkz.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fda86oc8rtm4cof9hbkwwkz.json
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@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"fda86oc8rtm4cof9hbkwwkz","title":"2023-03-15","desc":"","updated":1678873177770,"created":1678867781167,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.03.15","type":"note","vault":{"fsPath":"vault"},"contentHash":"b97cec0f8c85a982d18bfffe21d74bd8","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":23,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":25,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":27,"column":0,"depth":2},"presnetation-edourad":{"type":"header","text":"Presnetation Edourad","value":"presnetation-edourad","line":29,"column":0,"depth":4},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":74,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":77,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":78,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":81,"column":0,"depth":2}},"children":[],"parent":"i0g2v1iyomcgc3cljv08h2n","data":{}},"body":"
2023-03-15
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.03.15
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
not category of plants ! (ways to access biodiversity)
\n
\n
\n
Say that DBGI is a Pilot
\n
\n
some numbers regarding the diversity of BG
\n
\n
What is a Knowledge Graph ?\nWhat is an Ontology ?
\n
\n
make a precision regarding the Open Science aspects (not only at the publication step but really Open Notebook Science)
\n
\n
\n
\n
Phylogeny /should be taxonomy
\n
\n
\n
A small transition sentence.\nNow I am going to talk you about what I started doing in my Bachelor work and what I am currently doing in my master
\n
\n
\n
Why ? do you make maps ?
\n
\n
\n
Explain very quickly what are the layers for
\n
\n
\n
You say you take a picture of the QR code and this updates the code automatically (explain why this is interesting)
\n
\n
\n
Community curation : here also explain quickly why this is nice !
\n
\n
\n
API what is that ??? You should explain to people how dont use computer
\n
\n
\n
12 Euros ... maybe not required +
\n
\n
\n
More than a collection tool its a set of tools or framework
\n
\n
\n
\n
\"unknowing\" system
\n
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fj70x7r26tmlekfouvpc73t.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fj70x7r26tmlekfouvpc73t.json
new file mode 100644
index 0000000000..3185d87765
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fj70x7r26tmlekfouvpc73t.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"fj70x7r26tmlekfouvpc73t","title":"2023-05-30","desc":"","updated":1685538307575,"created":1685450346784,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.05.30","type":"note","vault":{"fsPath":"vault"},"contentHash":"f78cdca6849862b7425a58f69f129946","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"chatgpt-exchanges-leading-to-the-previous-selected-papers":{"type":"header","text":"ChatGPT exchanges leading to the previous selected papers","value":"chatgpt-exchanges-leading-to-the-previous-selected-papers","line":62,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":120,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":122,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":124,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":126,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":129,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":130,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":133,"column":0,"depth":2}},"children":[],"parent":"stmdzo7k7so0orxmyyqty4z","data":{}},"body":"
2023-05-30
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.05.30
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
A General Method for Simultaneously Accounting for Phylogenetic and Species Sampling Uncertainty via Rubin’s Rules in Comparative Analysis\nhttps://doi.org/10.1093/sysbio/syy089
ChatGPT exchanges leading to the previous selected papers
\n
What are the methods to construct (infer or expand) a full image from partial inputs (bits of the big picture). These methods should not involve automated learning.\nChatGPT\nConstructing or inferring a full image from partial inputs without involving automated learning can be challenging, as it typically requires complex computational algorithms or manual interventions. However, there are a few methods that can be used to reconstruct or expand a full image from partial inputs without relying on automated learning. Here are a few approaches:
\n
Patch-based methods: In this approach, the partial inputs or patches are analyzed individually, and then these patches are combined or stitched together to form the full image. This method requires a prior understanding of the spatial relationships between patches. Various algorithms, such as graph cuts or seam carving, can be used to combine the patches effectively.
\n
Image inpainting techniques: Image inpainting aims to fill in missing or occluded regions in an image. By applying inpainting algorithms, you can reconstruct the missing parts of the image based on the surrounding information or by propagating the existing image content. Techniques like texture synthesis, diffusion-based methods, or exemplar-based approaches can be used for image inpainting.
\n
Structure-from-Motion (SfM): SfM is a technique used to reconstruct 3D scenes from 2D image sequences. If you have partial inputs from different viewpoints or angles, you can use SfM algorithms to estimate the camera poses and 3D structure of the scene. By combining the reconstructed 3D information, you can generate a full image or a more complete representation of the scene.
\n
Image completion with manual interventions: If automated learning is not allowed, manual interventions can be used to complete or expand an image from partial inputs. This approach involves human interaction or expertise to fill in missing details or to infer the complete image based on the available information. Tools like image editing software can be employed to manually paint or draw missing parts of the image.
\n
It's important to note that these methods may require some level of computational algorithms or techniques, but they do not rely on automated learning specifically. Instead, they involve manual interventions or computational procedures that do not involve training on large datasets.
\n
Let's say that this patchy dataset is a table of occurence of molecules within living organisms. We thus have phylogenetic relationshsips across the organisms and chemical class taxonomy across the molecules. What approch would you propose to reconstruct a full dataset from a patchy dataset ?\nChatGPT\nIn the case of a patchy dataset representing the occurrence of molecules within living organisms, where phylogenetic relationships across organisms and chemical class taxonomy across molecules are known, you can leverage these relationships to reconstruct a more complete dataset. Here's an approach you can consider:
\n
Phylogenetic imputation: Given the phylogenetic relationships among organisms, you can utilize this information to infer missing values in the dataset. This approach assumes that closely related organisms have similar characteristics, including the occurrence of molecules. You can estimate missing values by propagating the observed data from closely related organisms to fill in the gaps in less studied or missing organisms.
\n
Chemical class-based imputation: If you have a taxonomy of chemical classes for the molecules, you can use this information to infer missing values. Explore the chemical classes present in the dataset and their relationships to impute missing occurrences based on the patterns observed within each class. This could involve considering the distribution of occurrences within a chemical class or using statistical measures within specific chemical class groups.
\n
Cross-validation: To enhance the reliability of the reconstructed dataset, you can perform cross-validation techniques. Split the available data into training and testing sets and use the known data to impute the missing values in the testing set. Then compare the imputed values with the actual values to evaluate the accuracy and adjust the imputation method if necessary.
\n
Expert validation: Given the complexity and domain-specific nature of the dataset, it is valuable to involve experts in the field. Experts can provide insights, validate the reconstructed dataset, and refine the imputation process based on their knowledge of the organisms, molecules, and their interactions.
\n
It's important to note that imputation methods rely on assumptions and might introduce some level of uncertainty. The quality and accuracy of the reconstructed dataset will depend on the availability and quality of the existing data, the accuracy of the phylogenetic relationships and chemical class taxonomy, and the effectiveness of the imputation methods employed.
\n
Overall, combining phylogenetic relationships, chemical class taxonomy, statistical imputation, and expert input can help you reconstruct a more complete dataset of molecule occurrences within living organisms.
\n
Great. Would their be an approach that could combine both the Phylogenetic imputation and the Chemical class-based imputation ? That is a method which would exploit the structure on both dimension of the datset for the inputation\nChatGPT\nYes, it is indeed possible to combine both phylogenetic imputation and chemical class-based imputation to exploit the structure on both dimensions of the dataset for imputation. Here's an approach that combines these two methods:
\n
Phylogenetic imputation: Use the phylogenetic relationships among organisms to propagate information and impute missing values. Start by identifying closely related organisms with available data. For each missing value, find the closest related organisms with observed data and use their values as a basis for imputation. This imputation process takes into account the assumption that closely related organisms share similar characteristics, including the occurrence of molecules.
\n
Chemical class-based imputation: Leverage the chemical class taxonomy to further refine the imputation process. Within each chemical class, observe the distribution of occurrences and utilize statistical measures such as mean, median, or mode to estimate missing values. Consider the patterns and tendencies within each chemical class while imputing missing values.
\n
Combination and refinement: Combine the imputed values from the phylogenetic imputation and chemical class-based imputation approaches. This can be achieved by assigning weights or merging the imputed values based on the confidence or reliability of each approach. You can also consider using statistical techniques such as ensemble methods or weighted averaging to combine the imputations effectively.
\n
Expert validation: As mentioned before, involving domain experts in the validation process is crucial. Experts can provide insights on the reliability and biological plausibility of the imputed values. They can also suggest adjustments or refinements to the imputation process based on their knowledge of the organisms, molecules, and their relationships.
\n
By combining phylogenetic imputation with chemical class-based imputation, you leverage both the phylogenetic relationships among organisms and the chemical class taxonomy of molecules to impute missing values. This approach takes advantage of the structural information present in both dimensions of the dataset, resulting in a more comprehensive and accurate imputation process.
\n
Paused
\n
Done
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fudihq4hmblgn1xkbepff7o.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fudihq4hmblgn1xkbepff7o.json
new file mode 100644
index 0000000000..2561dd0a13
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fudihq4hmblgn1xkbepff7o.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"fudihq4hmblgn1xkbepff7o","title":"2023-07-29","desc":"","updated":1690622960232,"created":1690622947908,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.07.29","type":"note","vault":{"fsPath":"vault"},"contentHash":"1348fc208686492a1d47828bd4c4f01a","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.07.29","id":"fudihq4hmblgn1xkbepff7o","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":26,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":27,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":29,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":31,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":33,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":35,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":37,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":40,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":41,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":44,"column":0,"depth":2}},"children":[],"parent":"p9uxp04cqx16vq7f9tvg8m8","data":{}},"body":"
2023-07-29
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.29
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fy9to4rrty69wn2nsrm86p7.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fy9to4rrty69wn2nsrm86p7.json
new file mode 100644
index 0000000000..8737cb3b27
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/fy9to4rrty69wn2nsrm86p7.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"fy9to4rrty69wn2nsrm86p7","title":"2023-10-12","desc":"","updated":1697192529832,"created":1697139493914,"traitIds":["open-notebook-commons-rouchene"],"custom":{},"fname":"open-notebook.commons.rouchene.2023.10.12","type":"note","vault":{"fsPath":"vault"},"contentHash":"d73f6e541077f88b5022f6cf5fa85d25","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.rouchene.2023.10.12","id":"fy9to4rrty69wn2nsrm86p7","vaultName":"vault"},"value":"projects.commons-public.microcosmics","position":{"start":{"line":14,"column":5,"offset":255},"end":{"line":14,"column":45,"offset":295},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"projects.commons-public.microcosmics"}}],"anchors":{"this-is-rimass-commons-lab-daily-open-notebook":{"type":"header","text":"This is Rimas's COMMONS Lab daily Open Notebook.","value":"this-is-rimass-commons-lab-daily-open-notebook","line":11,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":15,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":17,"column":0,"depth":3},"daily-work-on-the-microcosmics-project":{"type":"header","text":"Daily work on the Microcosmics project","value":"daily-work-on-the-microcosmics-project","line":20,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":25,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":26,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":28,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":30,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":32,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":34,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":36,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":39,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":40,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":43,"column":0,"depth":2}},"children":[],"parent":"6ji2eab9zcj88r3x8mn8edv","data":{}},"body":"
2023-10-12
\n
This is Rimas's COMMONS Lab daily Open Notebook.
\n
Today is 2023.10.12
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/g43owr98tuqbu79kjxi6yc6.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/g43owr98tuqbu79kjxi6yc6.json
new file mode 100644
index 0000000000..94adc2a8ac
--- /dev/null
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
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--- /dev/null
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gn90n64nlh04hkyvzdcnp4s.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gn90n64nlh04hkyvzdcnp4s.json
new file mode 100644
index 0000000000..b57172545c
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gn90n64nlh04hkyvzdcnp4s.json
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2023-08-29
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.08.29
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gvdyfgvq0z08fcfaqzmhtjo.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gvdyfgvq0z08fcfaqzmhtjo.json
new file mode 100644
index 0000000000..c8c09e90d0
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gvdyfgvq0z08fcfaqzmhtjo.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"gvdyfgvq0z08fcfaqzmhtjo","title":"Freedom","desc":"","updated":1653562088317,"created":1653562064628,"custom":{},"fname":"freedom","type":"note","vault":{"fsPath":"vault"},"contentHash":"011e15e4045990bffe8cbc58d31fbad2","links":[],"anchors":{},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Freedom
\n
La liberté académique est la base de la recherche et de l'enseignement. Elle consiste en “the right to freely define research questions, choose and develop theories, gather empirical material and employ sound academic research methods, to question accepted wisdom and bring forward new ideas. It entails the right to share, disseminate and publish the results thereof openly, including through training and teaching. It is the freedom of researchers to express their opinion without being disadvantaged by the system in which they work or by governmental or institutional censorship and discrimination.” Bonn declaration on freedom of academic research, Adopted at the Ministerial Conference on the European Research Area on 20 October.
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gwibrrzgsg8mb72ec1fwu2u.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gwibrrzgsg8mb72ec1fwu2u.json
new file mode 100644
index 0000000000..0eda531be0
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/gwibrrzgsg8mb72ec1fwu2u.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"gwibrrzgsg8mb72ec1fwu2u","title":"2023-07-25","desc":"","updated":1690268764725,"created":1690268749831,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.07.25","type":"note","vault":{"fsPath":"vault"},"contentHash":"083f5f13337ee1d0e7f353730093ba17","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.07.25","id":"gwibrrzgsg8mb72ec1fwu2u","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":28,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":29,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":31,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":33,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":35,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":37,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":39,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":42,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":43,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":46,"column":0,"depth":2}},"children":[],"parent":"p9uxp04cqx16vq7f9tvg8m8","data":{}},"body":"
2023-07-25
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.25
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/habtsdf8nwmm3oowinqhi6h.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/habtsdf8nwmm3oowinqhi6h.json
new file mode 100644
index 0000000000..d2b0d3cdb9
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/habtsdf8nwmm3oowinqhi6h.json
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+{"pageProps":{"note":{"id":"habtsdf8nwmm3oowinqhi6h","title":"Soil","desc":"","updated":1697466547810,"created":1697466535859,"custom":{},"fname":"projects.commons-public.microcosmics.metabolomics.soil","type":"note","vault":{"fsPath":"vault"},"contentHash":"50bb7bfff15f0e5452a0cf3cce36dbaf","links":[],"anchors":{"extraction":{"type":"header","text":"Extraction","value":"extraction","line":9,"column":0,"depth":3}},"children":[],"parent":"9nu26axhshlukejhh7yin28","data":{}},"body":"
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hpnaglyhnb48vuiniqecnqf.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hpnaglyhnb48vuiniqecnqf.json
new file mode 100644
index 0000000000..84bb4a4017
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hpnaglyhnb48vuiniqecnqf.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"hpnaglyhnb48vuiniqecnqf","title":"Nginx","desc":"","updated":1697209105175,"created":1655621752930,"custom":{},"fname":"nginx","type":"note","vault":{"fsPath":"vault"},"contentHash":"5c325e6acf12fc84a4807173be57c386","links":[],"anchors":{"title":{"type":"header","text":"Title","value":"title","line":8,"column":0,"depth":1},"context":{"type":"header","text":"Context","value":"context","line":10,"column":0,"depth":2},"need":{"type":"header","text":"Need","value":"need","line":15,"column":0,"depth":2},"task-of-the-noteparagraphtextpaperproject":{"type":"header","text":"Task (of the note/paragraph/text/paper/project)","value":"task-of-the-noteparagraphtextpaperproject","line":18,"column":0,"depth":2},"if-you-would-like-to-gzip-your-stuff":{"type":"header","text":"If you would like to gzip your stuff","value":"if-you-would-like-to-gzip-your-stuff","line":99,"column":0,"depth":1},"setup-the-proxy":{"type":"header","text":"Setup the proxy","value":"setup-the-proxy","line":104,"column":0,"depth":1},"this-will-forward-all-requests-to-the-server":{"type":"header","text":"This will forward all requests to the server","value":"this-will-forward-all-requests-to-the-server","line":105,"column":0,"depth":1},"and-then-it-will-relay-the-servers-response-back-to-the-client":{"type":"header","text":"and then it will relay the servers response back to the client","value":"and-then-it-will-relay-the-servers-response-back-to-the-client","line":106,"column":0,"depth":1},"object-of-the-noteparagraphtextpaperproject":{"type":"header","text":"Object (of the note/paragraph/text/paper/project)","value":"object-of-the-noteparagraphtextpaperproject","line":134,"column":0,"depth":2},"ressources":{"type":"header","text":"Ressources","value":"ressources","line":138,"column":0,"depth":2},"checking-nginx-status":{"type":"header","text":"Checking nginx status","value":"checking-nginx-status","line":187,"column":0,"depth":3},"to-serve-a-directory":{"type":"header","text":"to serve a directory","value":"to-serve-a-directory","line":217,"column":0,"depth":2},"dashboard":{"type":"header","text":"dashboard","value":"dashboard","line":273,"column":0,"depth":3},"setting-up-on-the-dbgi-vm":{"type":"header","text":"Setting up on the dbgi vm","value":"setting-up-on-the-dbgi-vm","line":280,"column":0,"depth":4}},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Nginx
\n
Title
\n
2022-11-02 14:42
\n
Context
\n
Looking into nginx to setup a connection to NocoDB from the commons_lab server
\n
This was done on the metabomaps server for the graphDB instance with the help of Jo.\nTrying to reproduce here.
\n
Need
\n
setup a connection to NocoDB from the commons_lab server
\n
Task (of the note/paragraph/text/paper/project)
\n
Third, indicate what you have done in an effort to address the need (this is the task).
Yeah !! But thats on the metabomaps server. Apparently thing will not work that smoothly on the commons server sinc it is behind the university firewall\nrunning (saved as a .sh script)\ncertbot --authenticator standalone --installer nginx -d xxxxxxx.xxxx.org --pre-hook \"service nginx stop\" --post-hook \"service nginx start\"
\n
\n
So I can serve the nocodb instance hosted on the commonslab server via a .dbgi.org domains
\n
\n
nginx server file is as follows
\n
server {\nlisten 80;\nlisten [::]:80;
\n
server_name xxxxx.dbgi.org;\n
\n
If you would like to gzip your stuff
\n
gzip on;\ngzip_min_length 1;\ngzip_types *;
\n
Setup the proxy
\n
This will forward all requests to the server
\n
and then it will relay the servers response back to the client
Saving debug log to /var/log/letsencrypt/letsencrypt.log\nRequesting a certificate for directus.dbgi.org
\n
Certbot failed to authenticate some domains (authenticator: standalone). The Certificate Authority reported these problems:\nDomain: directus.dbgi.org\nType: dns\nDetail: DNS problem: NXDOMAIN looking up A for directus.dbgi.org - check that a DNS record exists for this domain; DNS problem: NXDOMAIN looking up AAAA for directus.dbgi.org - check that a DNS record exists for this domain
\n
Hint: The Certificate Authority failed to download the challenge files from the temporary standalone webserver started by Certbot on port 80. Ensure that the listed domains point to this machine and that it can accept inbound connections from the internet.
\n
Of course it doesn't work as we need to declare the DNS first at our DNS provider interface lets go ther\nIt needs to be opened
\n
Done
\n
Then copied the nocodb in /etc/nginx/sites-enabled and changed the server name
\n
Certbox command is still not OK but different error.\nWebsite is accessible
\n
(base) allardpm@biolpc045600:/etc/nginx/sites-enabled$ sudo certbot --authenticator standalone --installer nginx -d directus.dbgi.org --pre-hook \"service nginx stop\" --post-hook \"service nginx start\"\nSaving debug log to /var/log/letsencrypt/letsencrypt.log\nRequesting a certificate for directus.dbgi.org
Hint: The Certificate Authority failed to download the challenge files from the temporary standalone webserver started by Certbot on port 80. Ensure that the listed domains point to this machine and that it can accept inbound connections from the internet.
\n
Some challenges have failed.\nAsk for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
\n
Checking nginx status
\n
systemctl status nginx
\n
on metabomaps it keeps falling.Here is an error message
\n
● nginx.service - A high performance web server and a reverse proxy server\nLoaded: loaded (/lib/systemd/system/nginx.service; enabled; vendor preset: enabled)\nActive: failed (Result: exit-code) since Mon 2022-10-17 19:05:49 UTC; 2 weeks 1 days ago\nDocs: man:nginx(8)\nProcess: 4655 ExecStartPre=/usr/sbin/nginx -t -q -g daemon on; master_process on; (code=exited, status=0/SUCCESS)\nProcess: 4656 ExecStart=/usr/sbin/nginx -g daemon on; master_process on; (code=exited, status=1/FAILURE)
\n
This is runned to check the nginy conf
\n
sudo nginx -t
\n
nginx: [warn] conflicting server name \"graph.metabomaps.com\" on 0.0.0.0:443, ignored\nnginx: [warn] conflicting server name \"graph.metabomaps.com\" on 0.0.0.0:80, ignored\nnginx: the configuration file /etc/nginx/nginx.conf syntax is ok\nnginx: configuration file /etc/nginx/nginx.conf test is successful
\n
## serving the directus interface foor the commons lab
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..6f531b30d4
--- /dev/null
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hz8tv9j28eyhbnggdklc9ch.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hz8tv9j28eyhbnggdklc9ch.json
new file mode 100644
index 0000000000..e25663e114
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/hz8tv9j28eyhbnggdklc9ch.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..605f4002c2
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new file mode 100644
index 0000000000..eec2b8b2d5
--- /dev/null
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ih6vyup3yre4m9woc9ldl7k.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ih6vyup3yre4m9woc9ldl7k.json
new file mode 100644
index 0000000000..122c4c08ba
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/irTDNBc18Lkt4qVIlhmew.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/irTDNBc18Lkt4qVIlhmew.json
new file mode 100644
index 0000000000..89f808ab08
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/irTDNBc18Lkt4qVIlhmew.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"irTDNBc18Lkt4qVIlhmew","title":"Scripts","desc":"","updated":1615593918205,"created":1615590768479,"custom":{},"fname":"wikidata.scripts","type":"note","vault":{"fsPath":"vault"},"contentHash":"e8b54850d34bb5a56f3bd0e9a0611df1","links":[],"anchors":{},"children":[],"parent":"59ftsVxFXXM9bB43vfKwK","data":{}},"body":"
Scripts
\n
How cool would this be to have a script allowing to automatically fetch the wikidata link and id of any selected word.\nThis would clearly facilitate the addition of wd links in manuscripts and documents. Such script could facilitate the use of wd while exploring a given topic. Ideally a small snapshot of the wd article could be displayed.\nI have no idea of how doable this is.\nApperas cool to me at the moment (2021-03-13 00:17) might be full BS.
\n
\n
check for similar plugins using google or wikipedia\nMake a small project out of this ?\nTo discuss with Daniel.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itinl4oosihdr0r1gc1t929.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itinl4oosihdr0r1gc1t929.json
new file mode 100644
index 0000000000..ed69f5c140
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itinl4oosihdr0r1gc1t929.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"fname":"open-notebook.commons.pmallard.2023.04","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254239,"created":1697541254239,"id":"itinl4oosihdr0r1gc1t929","desc":"","links":[],"anchors":{},"children":["wsndq74fuck4q6ivovplr64","k7cx1lkd3sfs8int9kpt63h","9oj9c91gnuxqd9yq3izn4re","o10kwttunlssxa9nb75la2y","9qsbp81ci31s52m5xb3sf3t"],"parent":"i21nzdv2qeai9y201qhqgqg","data":{},"title":"04"},"body":"
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itn752r9fowkcb0j334am8b.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itn752r9fowkcb0j334am8b.json
new file mode 100644
index 0000000000..7baf9fffb3
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/itn752r9fowkcb0j334am8b.json
@@ -0,0 +1 @@
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/j4e9zoyjabmni4clkq82wl8.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/j4e9zoyjabmni4clkq82wl8.json
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index 0000000000..2eff105734
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/j4e9zoyjabmni4clkq82wl8.json
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+{"pageProps":{"note":{"id":"j4e9zoyjabmni4clkq82wl8","title":"2023-02-24","desc":"","updated":1677220281855,"created":1677220271593,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.02.24","type":"note","vault":{"fsPath":"vault"},"contentHash":"f60f2b686e47984d9e728286f2770ab7","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":23,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":25,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":27,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":29,"column":0,"depth":2},"upload-the-si-of-james-lever-paper-to-wikidata":{"type":"header","text":"Upload the SI of James Lever paper to Wikidata","value":"upload-the-si-of-james-lever-paper-to-wikidata","line":31,"column":0,"depth":3},"-2":{"type":"header","text":"","value":"-2","line":35,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":36,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":39,"column":0,"depth":2}},"children":[],"parent":"lfbf5wm17i4p47xjbd6i6w4","data":{}},"body":"
2023-02-24
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.02.24
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/jldFUSJGjDf1mFH8c2yUI.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/jldFUSJGjDf1mFH8c2yUI.json
new file mode 100644
index 0000000000..99cb959682
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/jldFUSJGjDf1mFH8c2yUI.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k2ZyWqz1dvbZP4gWGXlzf.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k2ZyWqz1dvbZP4gWGXlzf.json
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index 0000000000..bf3c879cb6
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Labbook
\n
Exercice 1
\n
docker run -it ubuntu
\n
root@ed76dc41b28c:/# figlet 'SIB courses are great!'
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k43g9w49ka7t67k3epgdw10.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k43g9w49ka7t67k3epgdw10.json
new file mode 100644
index 0000000000..d78cc4a8e4
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k7cx1lkd3sfs8int9kpt63h.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k7cx1lkd3sfs8int9kpt63h.json
new file mode 100644
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--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/k7cx1lkd3sfs8int9kpt63h.json
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2023-04-22
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.04.22
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kj9v4h6p9gaypzlvdij6feg.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kj9v4h6p9gaypzlvdij6feg.json
new file mode 100644
index 0000000000..6ddb655d04
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kj9v4h6p9gaypzlvdij6feg.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kxfjq6ehd8eo6o1wxcff1cr.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kxfjq6ehd8eo6o1wxcff1cr.json
new file mode 100644
index 0000000000..9997aa6b5c
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kxfjq6ehd8eo6o1wxcff1cr.json
@@ -0,0 +1 @@
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2023-07-01
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.01
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kymn3h64uphg9lwkh9powmv.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kymn3h64uphg9lwkh9powmv.json
new file mode 100644
index 0000000000..795fe0bc15
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kymn3h64uphg9lwkh9powmv.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"kymn3h64uphg9lwkh9powmv","title":"20","desc":"","updated":1677601214281,"created":1677601214281,"custom":{},"fname":"open-notebook.commons.sguetchueng.2023.02.20","type":"note","vault":{"fsPath":"vault"},"contentHash":"9704d7e582ca0ffb41ac9f62810ee0ad","links":[],"anchors":{},"children":[],"parent":"36354ldtt6g7yq3uvrjykle","data":{}},"body":"
20
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kypyoyh6fs25q16mhc0w4jr.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kypyoyh6fs25q16mhc0w4jr.json
new file mode 100644
index 0000000000..e3e17d82c2
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kypyoyh6fs25q16mhc0w4jr.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"kypyoyh6fs25q16mhc0w4jr","title":"2023-03-08","desc":"","updated":1678282470972,"created":1678282282589,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.03.08","type":"note","vault":{"fsPath":"vault"},"contentHash":"059dea5d9f13c6df37b21c294eebeb9a","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":16,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":19,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":22,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":26,"column":0,"depth":2}},"children":[],"parent":"oxbyb3iqmrqrlvwrlt40q4m","data":{}},"body":"
2023-03-08
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.08
\n
Notes
\n
Todo today
\n
\n
find a good nomenclature for n dimensional data
\n
\n
Doing
\n
Done
\n
\n
Hastings ratio for α and μ
\n
\n
Todo tomorrow
\n
\n
check ratios with Daniel
\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kzei5nishi0yuojckqly29b.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kzei5nishi0yuojckqly29b.json
new file mode 100644
index 0000000000..aaac679b29
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/kzei5nishi0yuojckqly29b.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/l0fc05g2ah4l8pad3st4u6r.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/l0fc05g2ah4l8pad3st4u6r.json
new file mode 100644
index 0000000000..92beaceffb
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/l0fc05g2ah4l8pad3st4u6r.json
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+{"pageProps":{"note":{"id":"l0fc05g2ah4l8pad3st4u6r","title":"2023-03-28","desc":"","updated":1680015372784,"created":1680015238223,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.03.28","type":"note","vault":{"fsPath":"vault"},"contentHash":"fc04f61372c849df8c8a000a83eaa3b3","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo":{"type":"header","text":"Todo","value":"todo","line":16,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":24,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":27,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":31,"column":0,"depth":2}},"children":[],"parent":"oxbyb3iqmrqrlvwrlt40q4m","data":{}},"body":"
2023-03-28
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.28
\n
Notes
\n
Todo
\n
\n
simulate ϵc from multivariate normal distribution with mean = 0 and cov prob_sigma
\n
from x simulate Lotus from x and P and Q --> R
\n
from R draw Bernoulli with P = R
\n
--> simulated data
\n
from simulated data try to do the opposite :\n
\n
try to infer γ and δ from MCMC --> should find our δ and γ
\n
\n
\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/lc23hwq5j8vqor58i2ab0fx.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/lc23hwq5j8vqor58i2ab0fx.json
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12
\n
This is Marco's daily open-notebook.
\n
Today is 2023.07.12
\n
Notes
\n
DBGI workshop
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/lfbf5wm17i4p47xjbd6i6w4.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/lfbf5wm17i4p47xjbd6i6w4.json
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index 0000000000..1f758e3a83
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/lfbf5wm17i4p47xjbd6i6w4.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ltir06xpwairswiznqobvbe.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ltir06xpwairswiznqobvbe.json
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2023-03-15
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.15
\n
Edouard's presentation
\n
DBGI is part of Earth metabolome initiative. Edouard is mainly in the wet lab part.
\n
\n
Right now they are transitioning from DBGI to Earth metabolome initiative (EMI).
\n
\n
Notes
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n
Learned Snakemake. It's actually super easy and it's super powerful to create reproducible workflows.
\n
\n
Todo tomorrow
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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2023-05-17
\n
This is Marco's daily open-notebook.
\n
Today is 2023.05.17
\n
Notes
\n
Markov random fields
\n
If we have a tree structure we can do either do \"loopy belief propagation\" which is updating all node one at a time. This is garanteed to converge to correct marginals but it is wasteful. There is an other way : \"collect and distribute schedule\". The idea is to pick one node as the \"root\" fo the tree, find all the leaves of the graph and compute messages to their parents. Continue until you reach the root. If the graph is a tree, any node can be a root. We then backpropagate back to the leaves. Advantage : we only do one update per message. See explanation here at 11min34sec. This is very similar to an HMM and its forward-backward algorithm.
\n
Now the problem for our model is that we have to combine two trees. The one from species and the one from molecules. We could think of each node as a combination of each molecule with each species.
\n
Todo today
\n
\n
look definition of loopy back propagation.
\n
Check out this blog. For more explanations. I think this new approach could really work for our case.
\n
Here is an implementation on an image. Could this be applied to our model ?
\n\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/m6cfdxbf5aemuecvobypkgn.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/m6cfdxbf5aemuecvobypkgn.json
new file mode 100644
index 0000000000..3bd5a39dea
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/m6cfdxbf5aemuecvobypkgn.json
@@ -0,0 +1 @@
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2023-09-26
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.09.26
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mqt1gcx2yuvpaoq5r99guwz.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mqt1gcx2yuvpaoq5r99guwz.json
new file mode 100644
index 0000000000..90a501bfd6
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mqt1gcx2yuvpaoq5r99guwz.json
@@ -0,0 +1 @@
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2023-06-23
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.23
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
Started at 2023-06-23 15:11\nFinished at 2023-06-23 15:28
\n
\n
\n
Doing
\n
Paused
\n
Done
\n
Notes
\n
Todo tomorrow, one day ... or never
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mz59v1zr7grqghkinjmk034.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mz59v1zr7grqghkinjmk034.json
new file mode 100644
index 0000000000..4105d12f85
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/mz59v1zr7grqghkinjmk034.json
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Open Notebook Mvisan
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This is Marco's daily open-notebook.
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Today is {{ CURRENT_YEAR }}.{{ CURRENT_MONTH }}.{{ CURRENT_DAY }}
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Notes
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Todo today
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Doing
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Done
\n
\n\n
\n
Todo tomorrow
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/n34ek93pt2py6moj7lvq9sf.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/n34ek93pt2py6moj7lvq9sf.json
new file mode 100644
index 0000000000..1f9e5272a9
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/n34ek93pt2py6moj7lvq9sf.json
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new file mode 100644
index 0000000000..40941c4597
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nk6tvsh1jsfmuynw74h6ztu.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nk6tvsh1jsfmuynw74h6ztu.json
new file mode 100644
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--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nk6tvsh1jsfmuynw74h6ztu.json
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2023-06-13
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.13
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmnpsy2e1rwqnqgurogi2u6.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmnpsy2e1rwqnqgurogi2u6.json
new file mode 100644
index 0000000000..d06c36c832
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmnpsy2e1rwqnqgurogi2u6.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmu1iz31fswfdevezly3un2.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmu1iz31fswfdevezly3un2.json
new file mode 100644
index 0000000000..8885849dce
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/nmu1iz31fswfdevezly3un2.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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new file mode 100644
index 0000000000..1fc58d7cd8
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/o10kwttunlssxa9nb75la2y.json
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Actually it could be a bad idea to duplicate a manubot repo and maybe the best way to go it to follow the establishment of a new repo.\nWill create one for Lendita report\nAnd think of a tuto is the instructions on manubot's website are not clear enough\nhttps://github.com/manubot/rootstock/blob/main/SETUP.md
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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+{"pageProps":{"note":{"id":"o4vyqs1dmdz6umqfkc2iwwt","title":"Ressources","desc":"","updated":1663411939645,"created":1663408071043,"custom":{},"fname":"lod.kg.ressources","type":"note","vault":{"fsPath":"vault"},"contentHash":"e7a1f93d48e7f070aaa558d7d902928c","links":[{"type":"wiki","from":{"fname":"lod.kg.ressources","id":"o4vyqs1dmdz6umqfkc2iwwt","vaultName":"vault"},"value":"people.sanya-bathla-taneja","position":{"start":{"line":35,"column":4,"offset":1280},"end":{"line":35,"column":34,"offset":1310},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"people.sanya-bathla-taneja"}}],"anchors":{"pheknowlator":{"type":"header","text":"PheKnowLator","value":"pheknowlator","line":8,"column":0,"depth":1},"kg-hub":{"type":"header","text":"KG-Hub","value":"kg-hub","line":18,"column":0,"depth":1},"napdi-kg":{"type":"header","text":"NaPDI-KG","value":"napdi-kg","line":28,"column":0,"depth":1}},"children":[],"parent":"cm7lxhcj1gc5cubsyzd3811","data":{}},"body":"
Ressources
\n
PheKnowLator
\n
What is PheKnowLator?\nPheKnowLator (Phenotype Knowledge Translator) or pkt_kg is the first fully customizable knowledge graph (KG) construction framework enabling users to build complex KGs that are Semantic Web compliant and amenable to automatic Web Ontology Language (OWL) reasoning, generate contemporary property graphs, and are importable by today’s popular graph toolkits. Please see the project Wiki for additional information.
NaPDI-KG is a knowledge graph framework to identify and generate mechanistic hypotheses for pharmacokinetic natural product-drug interactions (NPDIs). This repository has been forked from the Knowledge-Graph-Hub. NaPDI-KG uses the PheKnowLator ecosystem to create the ontology-grounded KG and the KG-Hub ecosystem to integrate the nodes and edges extracted from natural product-related biomedical literature. NaPDI-KG includes the following components -
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ordhq65nfz0cco816cjh1mw.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ordhq65nfz0cco816cjh1mw.json
new file mode 100644
index 0000000000..3fc318a108
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ordhq65nfz0cco816cjh1mw.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"fname":"daily.notebook.pma.2023.02","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254231,"created":1697541254231,"id":"ordhq65nfz0cco816cjh1mw","desc":"","links":[],"anchors":{},"children":["gh2ulxcnf4rrw2ifoq2i7cc"],"parent":"9rdwrsd8asjnhvcvnhy2fcn","data":{},"title":"02"},"body":"
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ovslc641d0h00s16tf6kl8w.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ovslc641d0h00s16tf6kl8w.json
new file mode 100644
index 0000000000..27da34cccc
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ovslc641d0h00s16tf6kl8w.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"ovslc641d0h00s16tf6kl8w","title":"Welcome","desc":"","updated":1693043602601,"created":1693041159856,"custom":{},"fname":"welcome","type":"note","vault":{"fsPath":"vault"},"contentHash":"2cea949b2d04c21f1ad07c2e4c75230a","links":[{"type":"wiki","from":{"fname":"welcome","id":"ovslc641d0h00s16tf6kl8w","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":42,"column":118,"offset":1701},"end":{"line":42,"column":149,"offset":1732},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":15,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":19,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":21,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":23,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":29,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":34,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":51,"column":0,"depth":2}},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Welcome
\n
Welcome the the COMMONS Lab Open Dendron.
\n
In the COMMONS Lab we intent to follow the Open Notebook Science approach to document our research.
\n
For this we use the Dendron system as a mean to efficiently capture notes and publish them.
\n
What is this note
\n
This note is a succinct tutorial note aiming to get you started in the use of the DBGI Dendron.
\n
Tutorial
\n
Dendron.
\n
What is Dendron ?
\n
\n
Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
\n
Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.
\n
\n
Where to get more info on Dendron ?
\n
\n
You can get more information in the Dendron system at the official website www.dendron.so
\n
All the Dendron documentation is hosted here https://wiki.dendron.so/ . It is, obviously, a Dendron itself.
\n
\n
Concrete steps to access and contribute to the DBGI Dendron
Voila ! You should now be in the COMMONS Lab Open Dendron.
\n
\n\n
Feel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at Setup
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..526a1e312c
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/oxbyb3iqmrqrlvwrlt40q4m.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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Guidelines for submitting a synopsis to Natural Product Reports
\n
NPR articles are designed to give an interesting insight into the topic, focussing on the key developments that have shaped a field rather than giving a very comprehensive overview of all results. Authors are encouraged to include their own perspective on developments, trends and future directions.\nBefore commissioning articles for NPR we ask that authors provide a brief synopsis. This is circulated to members of the editorial board for comment.
\n
Please include the following information in your synopsis:
\n\n
A proposed title for the work
\n\n\n
Authors and affiliations (including co-authors if known)
A brief description of the review and topic to be covered, including:
\n
\n
\n
What the implications are for the wider scientific community
\n
\n
\n
Which communities your article will appeal to
\n
\n
\n
\n
\n
Suggested section headings
\n
\n\n\n
A brief list of key references, noting any other reviews which have been published in the area.
\n\n
\n
\n
Adriano Rutz, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G Graham, Ralf Stephan, Roderic Page, Jiří Vondrášek, Christoph Steinbeck, Guido F Pauli, Jean-Luc Wolfender, Jonathan Bisson, Pierre-Marie Allard (2022) The LOTUS initiative for open knowledge management in natural products research eLife 11:e70780 https://doi.org/10.7554/eLife.70780
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..d7efb740c7
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/p9uxp04cqx16vq7f9tvg8m8.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/pdbawzx5mh1mz7n8umxwqvw.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/pdbawzx5mh1mz7n8umxwqvw.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/peu48qaje9ypewkhiyt8ki8.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/peu48qaje9ypewkhiyt8ki8.json
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/peu48qaje9ypewkhiyt8ki8.json
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2023-02-28
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.28
\n
Notes
\n
Watched Madleina's presentation on presentation about sex determination
\n
let us denote nic the number of reads in individual i in contig c. We have :
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/po2nsu5o5dw785worh1j47p.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/po2nsu5o5dw785worh1j47p.json
new file mode 100644
index 0000000000..d75d7b5a32
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/po2nsu5o5dw785worh1j47p.json
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2023-09-02
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.09.02
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qcUnyE9eaS2PVPPngKeB1.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qcUnyE9eaS2PVPPngKeB1.json
new file mode 100644
index 0000000000..fa1cb3021d
--- /dev/null
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Sparql
\n
SPARQL queries
\n
all compounds produced by a given taxon or group of taxa (including children taxa) :
This SPAQRL query is based on a proposition of Jakub Galgonek jakub.galgonek@uochb.cas.cz (https://idsm.elixir-czech.cz/) and adapted by Pierre-Marie Allard (pierre-marie.allard@unige.ch)\nIt returns an order list of organisms known to produce chemical compounds having an indolic moiety.\nThe organisms are aggregated at the parent taxon level, and the list is ordered by number of compound occurence in the parent t
SELECTDISTINCT?parent_taxon?parent_taxon_name?compound?interaction?compoundLabel?geneLabel?biological_processLabel?diseaseLabelWHERE{\n #?compound wdt:P2868 ?mesh.\n #?mesh wdt:P486 \"D000962\".\n ?compoundwdt:P235?inchikey.\n {\n ?compoundp:P703?statement.\n ?statementps:P703?taxon.\n ?taxonwdt:P171?parent_taxon.\n OPTIONAL{?taxonwdt:P171?parent_taxon.}\n OPTIONAL{?parent_taxonwdt:P225?parent_taxon_name.}\n {\n ?statementprov:wasDerivedFrom?ref.\n ?refpr:P248?reference.\n ?referencewdt:P356?reference_doi;\n wdt:P1476?reference_title.\n }\n #?compound p:P129 ?interaction.\n #?interaction wdt: wd:Q21119831.\n \n ?compoundwdt:P129?gene_product.# drug interacts with a gene_product\n ?genewdt:P688?gene_product.# gene_product (usually a protein) is a product of a gene (a region of DNA)\n ?diseasewdt:P2293?gene.# genetic association between disease and gene\n ?diseasewdt:P279* wd:Q12078.# limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)\n ?gene_productwdt:P682?biological_process.#add information about the GO biological processes that the gene is related to \n\n ?biological_process(wdt:P361|wdt:P279)* wd:Q14599311.\n }\n SERVICEwikibase:label{bd:serviceParamwikibase:language\"[AUTO_LANGUAGE],en\".}\n}\n \nGROUPBY?parent_taxon?parent_taxon_name?compound?interaction?compoundLabel?geneLabel?biological_processLabel?diseaseLabel\n#ORDER BY DESC (?count)\n
#title (Private): Which are the available referenced structure-organism pairs on Wikidata? (example limited to 1000 results)\nSELECT DISTINCT ?structure ?structure_inchikey ?taxon ?taxon_name ?reference ?reference_doi WHERE {\n?structure wdt:P235 ?structure_inchikey; # get the inchikey\np:P703[ # statement found in taxon\nps:P703 ?taxon; # get the taxon\n(prov:wasDerivedFrom/pr:P248) ?reference ]. # get the reference\n?taxon wdt:P225 ?taxon_name. # get the taxon scientific name\n?reference wdt:P356 ?reference_doi. # get the reference DOI\n}\nLIMIT 10
SELECT ?chemical_compound ?compoundLabel ?queried_taxa ?queried_taxaLabel ?queried_taxall ?queried_taxallLabel ?pfcode WHERE {
\n
SERVICE https://query.wikidata.org/sparql {\nVALUES ?queried_taxa {\nwd:Q310915\n}\n{\n?chemical_compound p:P703 ?stmt.# We selecte chemical classes having the found in taxon statement\n?queried_taxall wdt:P171* ?queried_taxa.\n?stmt ps:P703 ?queried_taxall. # and the restrict the found in taxon statement to match our queried taxa\n}\n?chemical_compound rdfs:label ?compoundLabel.\n?queried_taxa rdfs:label ?queried_taxaLabel.\n?queried_taxall rdfs:label ?queried_taxallLabel.
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qftdp14ffcpbr9dixsq7xdk.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qftdp14ffcpbr9dixsq7xdk.json
new file mode 100644
index 0000000000..b6e0230f7d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qftdp14ffcpbr9dixsq7xdk.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"qftdp14ffcpbr9dixsq7xdk","title":"2023-07-05","desc":"","updated":1688541774786,"created":1688541751356,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.07.05","type":"note","vault":{"fsPath":"vault"},"contentHash":"a60337c074b70f92c3d496e44e412c3b","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.07.05","id":"qftdp14ffcpbr9dixsq7xdk","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":26,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":27,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":29,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":31,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":33,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":35,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":37,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":40,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":41,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":44,"column":0,"depth":2}},"children":[],"parent":"p9uxp04cqx16vq7f9tvg8m8","data":{}},"body":"
2023-07-05
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.07.05
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qgqilgm1adepqhb6y1xrjuq.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qgqilgm1adepqhb6y1xrjuq.json
new file mode 100644
index 0000000000..c3fc3cd844
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qgqilgm1adepqhb6y1xrjuq.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..80033aedf6
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qyh8bc7jfc6ac1512y4h6yb.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qyh8bc7jfc6ac1512y4h6yb.json
new file mode 100644
index 0000000000..0faf36fbae
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qyh8bc7jfc6ac1512y4h6yb.json
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+{"pageProps":{"note":{"id":"qyh8bc7jfc6ac1512y4h6yb","title":"Logbook","desc":"","updated":1646495532791,"created":1646495350227,"custom":{},"fname":"canopus.logbook","type":"note","vault":{"fsPath":"vault"},"contentHash":"de431345d1d5b0cc2d4bf76d14dc6656","links":[],"anchors":{},"children":[],"parent":"ih6vyup3yre4m9woc9ldl7k","data":{}},"body":"
Logbook
\n
following http://localhost:8888/notebooks/Tutorial.ipynb
\n
(installed cli on laptop but too slow)\nworking on commons_server
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qyxwa1l9hfoi9d8pis7v98l.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qyxwa1l9hfoi9d8pis7v98l.json
new file mode 100644
index 0000000000..fce836b407
--- /dev/null
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@@ -0,0 +1 @@
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Pmallard
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is {{ CURRENT_YEAR }}.{{ CURRENT_MONTH }}.{{ CURRENT_DAY }}
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzcz2txf8699jx340tvf33v.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzcz2txf8699jx340tvf33v.json
new file mode 100644
index 0000000000..30b9a90847
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzcz2txf8699jx340tvf33v.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"qzcz2txf8699jx340tvf33v","title":"2023-02-13","desc":"","updated":1676307490039,"created":1676280398443,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.02.13","type":"note","vault":{"fsPath":"vault"},"contentHash":"f298b12555164d3796fde17a76b7bc2c","links":[{"type":"ref","from":{"fname":"open-notebook.commons.mvisani.2023.02.13","id":"qzcz2txf8699jx340tvf33v","vaultName":"vault"},"value":"A","position":{"start":{"line":10,"column":1,"offset":269},"end":{"line":10,"column":7,"offset":275},"indent":[]},"xvault":false,"to":{"fname":"A"}}],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":13,"column":0,"depth":2},"":{"type":"header","text":"","value":"","line":20,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":21,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":23,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":25,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":27,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":29,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":31,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":33,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":34,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":35,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":38,"column":0,"depth":2}},"children":[],"parent":"f7kju6sk6wivpqr1onnfy4u","data":{}},"body":"
2023-02-13
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.13
\n
Todo today
\n
\n
try to write out complete model (try to be as general as possible )
\n
continue C++ courses
\n
figure out a way to add the LaTex mathematical model in Dendron in order for people to access it
\n
\n
\nNo note with name A found in cache during parsing.\n
\n
\n
\n
Doing
\n
Paused
\n
Done
\n
\n
ask how to access MS data and how to pass to to the 1 and 0 matrix
\n
\n
Notes
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzrcu3l4nnq3eikp3vpjvqd.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzrcu3l4nnq3eikp3vpjvqd.json
new file mode 100644
index 0000000000..32cfc9c743
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/qzrcu3l4nnq3eikp3vpjvqd.json
@@ -0,0 +1 @@
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2023-03-12
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.03.13
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r3rc6aeclin5kl4mw7002fr.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r3rc6aeclin5kl4mw7002fr.json
new file mode 100644
index 0000000000..576be38a79
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r3rc6aeclin5kl4mw7002fr.json
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+{"pageProps":{"note":{"id":"r3rc6aeclin5kl4mw7002fr","title":"2023-06-22","desc":"","updated":1687412679874,"created":1687411812677,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.06.22","type":"note","vault":{"fsPath":"vault"},"contentHash":"a7644d720d7026414b0fda06e74017c1","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.06.22","id":"r3rc6aeclin5kl4mw7002fr","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":31,"column":22,"offset":975},"end":{"line":31,"column":35,"offset":988},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":23,"column":0,"depth":3},"plan":{"type":"header","text":"Plan","value":"plan","line":34,"column":0,"depth":3},"paused":{"type":"header","text":"Paused","value":"paused","line":50,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":52,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":54,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":56,"column":0,"depth":2},"-3":{"type":"header","text":"","value":"-3","line":59,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":60,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":63,"column":0,"depth":2}},"children":[],"parent":"9y2owvmuwe3k3aj7q730usn","data":{}},"body":"
2023-06-22
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.22
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
I have been contacted by an editor of Natural Products Reports proposing to write a Viewpoint paper on Open Science in natural products research.\nI am interested but have some fear in committing to yet another project given the current list of running tasks.
\n
I have decide to give it a try but following this method.\nI'll work on this project by small chunks of 15 min daily. No more, no less. This will also be a methodological experiment.
\n
Got inspired by this article in Science (find ref)
\n
Plan
\n
Today I'll set up the template for note taking for this project and will answer the email of the editor.\nActually I might not need to create yet another daily template. And will keep notes in this one.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r46x7sdh6q4btsy6mp62rkp.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r46x7sdh6q4btsy6mp62rkp.json
new file mode 100644
index 0000000000..9eab993174
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/r46x7sdh6q4btsy6mp62rkp.json
@@ -0,0 +1 @@
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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new file mode 100644
index 0000000000..f9784efbc1
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/rvqeqbxn9m3a62ibrbufszk.json
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See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sbfuh96mq7lxrzznz5lny1l.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sbfuh96mq7lxrzznz5lny1l.json
new file mode 100644
index 0000000000..4413e93320
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sbfuh96mq7lxrzznz5lny1l.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sk4m9gq7vz2t9phcxlxvqpw.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sk4m9gq7vz2t9phcxlxvqpw.json
new file mode 100644
index 0000000000..1c1b16a479
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/sk4m9gq7vz2t9phcxlxvqpw.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"sk4m9gq7vz2t9phcxlxvqpw","title":"Utils","desc":"","updated":1695111295728,"created":1695111295728,"custom":{},"fname":"utils","type":"note","vault":{"fsPath":"vault"},"contentHash":"6633325a2589c1f5db9b1c938f769ec8","links":[],"anchors":{},"children":["t22kyc0u219zttxwumy1mz4"],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/spcjavj3vg70loxndmjroo2.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/spcjavj3vg70loxndmjroo2.json
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--- /dev/null
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@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"spcjavj3vg70loxndmjroo2","title":"Setup","desc":"","updated":1693043762046,"created":1693042918607,"custom":{},"fname":"open-notebook.commons.setup","type":"note","vault":{"fsPath":"vault"},"contentHash":"1f7e4c30823fbb2b69a73cbcb82af0b8","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.setup","id":"spcjavj3vg70loxndmjroo2","vaultName":"vault"},"value":"templates.open-notebook.commons.pmallard","position":{"start":{"line":59,"column":27,"offset":1957},"end":{"line":59,"column":71,"offset":2001},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"templates.open-notebook.commons.pmallard"}},{"from":{"id":"ovslc641d0h00s16tf6kl8w","fname":"welcome","vaultName":"vault"},"type":"backlink","position":{"start":{"line":42,"column":118,"offset":1701},"end":{"line":42,"column":149,"offset":1732},"indent":[]},"value":"open-notebook.commons.setup"},{"from":{"id":"QvYK9hGbCvPpEfSRYhV8j","fname":"root","vaultName":"vault"},"type":"backlink","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"value":"open-notebook.commons.setup"}],"anchors":{"defining-a-note-trait-for-daily-logs":{"type":"header","text":"Defining a Note trait for daily logs","value":"defining-a-note-trait-for-daily-logs","line":10,"column":0,"depth":3},"set-the-notes-trait":{"type":"header","text":"Set the Notes trait","value":"set-the-notes-trait","line":17,"column":0,"depth":4},"edit-the-template":{"type":"header","text":"Edit the template.","value":"edit-the-template","line":62,"column":0,"depth":4},"set-a-keyboard-shortcut":{"type":"header","text":"Set a keyboard shortcut","value":"set-a-keyboard-shortcut","line":68,"column":0,"depth":4}},"children":[],"parent":"ne6ca7ufq0o7dqjc8q2ilnk","data":{}},"body":"
Create a new Note Trait\nRun the command Dendron: Configure Note Traits. Give your new trait a unique name. In this example, we'll call the trait open-notebook-pma. Hit Enter and a open-notebook-pma.js file will appear in your editor. This is where you define your custom trait logic.
\n
\n
\n
Add the trait behavior\nAdd in Javascript code to have custom settings when creating the note name and the note title.
\n
\n\n
Here we used
\n
module.exports={\n OnWillCreate:{\n /**\n * This example sets a prefix of 'planning', and then adds a date hierarchy\n * using the luxon module.\n */\n setNameModifier(){\n // This example sets a prefix of 'planning', and then adds a date\n // hierarchy using the luxon module.\n return{\n name:\"open-notebook-commons.pma.\"+ luxon.DateTime.local().toFormat(\"yyyy.MM.dd\"),\n promptUserForModification:true,\n };\n },\n },\n OnCreate:{\n setTitle(props){\n // This example will use the currentNoteName property, extract the\n // yyyy.MM.dd date portion of the note name, and then reformat it with\n // dashes.\n return props.currentNoteName.split(\".\").slice(-3).join(\"-\");\n },\n /**\n * Apply a template to each note. NOTE: If you want to use this code, you\n * will need a note file called `templates.planning-template.md` in your\n * Dendron workspace.\n */\n setTemplate:()=>{\n return\"templates.open-notebook-pma\";\n },\n },\n};\n
\n
Edit the template.
\n
You can (optionally) have a template for your journal notes.\nHere I used the following Pmallard.\nThis template can be modified according to your needs.
\n
Set a keyboard shortcut
\n
I added a keyboard shortcut for it. But this needs to be done locally in your VSCode preferences (its not part of the published Dendron)\nFor this you can
\n\n
Run the VSCode Command Preferences: Open Keyboard Shortcuts (JSON) (Cmd+Shift + P)
\n
Add the following entry to the bottom of your keybindings.json file, with the shortcut key combo of your choice:\n{\n\"key\": \"cmd+o cmd+n\",\n\"command\": \"dendron.customCommand.open-notebook-pmallard\"\n}
\n\n
For example :
\n
\n
open-notebook-commons-pmallard.js
\n
\n
Adapt your keyboard shortcuts so that it leads to your own note traits.
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/stmdzo7k7so0orxmyyqty4z.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/stmdzo7k7so0orxmyyqty4z.json
new file mode 100644
index 0000000000..93af582e63
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/stmdzo7k7so0orxmyyqty4z.json
@@ -0,0 +1 @@
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..e1a1f26b7f
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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+{"pageProps":{"note":{"id":"t45ez4nn8jm6agjhegt7fhj","title":"Emergence","desc":"","updated":1664398406442,"created":1664396672587,"custom":{},"fname":"ool.emergence","type":"note","vault":{"fsPath":"vault"},"contentHash":"364cc0635c3f6c9e457922336fea17cc","links":[],"anchors":{"explaining-emergence-towards-an-ontology-of-levels":{"type":"header","text":"EXPLAINING EMERGENCE: TOWARDS AN ONTOLOGY OF LEVELS","value":"explaining-emergence-towards-an-ontology-of-levels","line":8,"column":0,"depth":1}},"children":[],"parent":"2cxr093kvrg4jojokwgqrbj","data":{}},"body":"
Emergence
\n
EXPLAINING EMERGENCE: TOWARDS AN ONTOLOGY OF LEVELS
\n
CLAUS EMMECHE, SIMO K0PPE and FREDERIK STJERNFELT
\n
The subject of this paper is the concept of emergence formulated as the idea that there are properties at a certain level of organization which can not be predicted from the properties found at lower levels.
\n
As far as we can see, there is a hidden and mostly unnoticed historical value in this \"coincidence\": the concept of emergence is exactly that reasonable aspect of vitalism which is worth to maintain.
\n
This is a very important difference between the vitalists and the emergentists: the vitalist's creative forces were relevant only in organic substances, not in inorganic matter. Emergence hence is creation of new properties regardless of the substance involved.
\n
But these system builders' discussions are very important, and they are one of the main reasons that the concept of emergence was \"devitalized\", that is, deprived of an immaterial causal agent.
\n
Emergence is among other things the concept which relate levels to each other - or to be more precise, the concept which denotes the very passage between them. It does not in itself solve anything, but it poses the problem in a general way, making it visible at the border of every specialized branch of science
\n
In Lloyd Morgan's definition of emergence as \"creation of new properties\" there are three key words: \"properties\", \"new\" and \"creation\". By a more detailed discussion of these key concepts, it is possible to grasp the primary topics in the concept of emergence.
\n
\n
properties
\n
\n
second, and more commonly used definition, tells us that emergence is at stake at the borders between the large sciences: where the explanatory power of one science must give in, another must take over at the level of the hitherto unexplainable - emergent - property. But it is not possible to restrict emergence to these borders. As already Morgan realized, the science usually considered more basic than all others - physics - in itself contains numerous cases of emergence.
\n
\n
novelty
\n
creation
\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/t99naq6lep530ii3s166vmg.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/t99naq6lep530ii3s166vmg.json
new file mode 100644
index 0000000000..380b0dd2c7
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/t99naq6lep530ii3s166vmg.json
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+{"pageProps":{"note":{"id":"t99naq6lep530ii3s166vmg","title":"2023-02-21","desc":"","updated":1676983378291,"created":1676974811810,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.02.21","type":"note","vault":{"fsPath":"vault"},"contentHash":"40f27555b74e445c820be43fbfee750b","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":14,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":16,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":25,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":31,"column":0,"depth":2}},"children":[],"parent":"f7kju6sk6wivpqr1onnfy4u","data":{}},"body":"
2023-02-21
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.21
\n
Notes
\n
Todo today
\n
\n
Find more littereture and read it
\n
Formlize discussion with Daniel
\n
\n
Doing
\n
\n
C++ lessons
\n
\n
Done
\n
\n
machine learning assignment
\n
discuss with Daniel details and following of the project.
\n
\n
Todo tomorrow
\n
\n
discuss with Pierre-Marie about \"new\" model and see if it could work with MS data that we have.
\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tc1xx5yh5fqrzyo3lpltuqi.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tc1xx5yh5fqrzyo3lpltuqi.json
new file mode 100644
index 0000000000..1b95399819
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tc1xx5yh5fqrzyo3lpltuqi.json
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+{"pageProps":{"note":{"fname":"projects.commons-public.microcosmics.rima","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254228,"created":1697541254228,"id":"tc1xx5yh5fqrzyo3lpltuqi","desc":"","links":[],"anchors":{},"children":["w817k3pc4gq7qpa9jdox5u7"],"parent":"0zmqus0478ehzat7p16a7sr","data":{},"title":"Rima"},"body":"
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/td03orht7dsxlg9rrde1tmv.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/td03orht7dsxlg9rrde1tmv.json
new file mode 100644
index 0000000000..cad7858f3d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/td03orht7dsxlg9rrde1tmv.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"td03orht7dsxlg9rrde1tmv","title":"2023-02-16","desc":"","updated":1676568390359,"created":1676530545924,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.02.16","type":"note","vault":{"fsPath":"vault"},"contentHash":"d76f6f1d092e545bb807188bb3113f15","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.02.16","id":"td03orht7dsxlg9rrde1tmv","vaultName":"vault"},"value":"tags.swat4hcls","alias":"#swat4hcls","position":{"start":{"line":15,"column":29,"offset":228},"end":{"line":15,"column":39,"offset":238},"indent":[]},"xvault":false,"to":{"fname":"tags.swat4hcls"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-xxxx-discussion-forum":{"type":"header","text":"Have a look at the XXXX discussion forum","value":"have-a-look-at-the-xxxx-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"4th-and-last-day-of-the-swat4hcls":{"type":"header","text":"4th and last day of the #swat4hcls","value":"4th-and-last-day-of-the-swat4hcls","line":23,"column":0,"depth":3},"hacking-scholia-for-custom-sparql-endpoints-discord":{"type":"header","text":"Hacking Scholia for custom SPARQL endpoints discord","value":"hacking-scholia-for-custom-sparql-endpoints-discord","line":30,"column":0,"depth":1},"creating-life-science-fom-wd":{"type":"header","text":"Creating life science fom WD","value":"creating-life-science-fom-wd","line":87,"column":0,"depth":1},"discussion-with-tarcisio-ana--marco":{"type":"header","text":"Discussion with Tarcisio, Ana & Marco","value":"discussion-with-tarcisio-ana--marco","line":90,"column":0,"depth":3},"this-is-my-nanopub-intro-page":{"type":"header","text":"This is my nanopub intro page","value":"this-is-my-nanopub-intro-page","line":108,"column":0,"depth":1},"paused":{"type":"header","text":"Paused","value":"paused","line":116,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":118,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":120,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":122,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":124,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":125,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":126,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":129,"column":0,"depth":2}},"children":[],"parent":"lfbf5wm17i4p47xjbd6i6w4","data":{}},"body":"
Hacking Scholia for custom SPARQL endpoints discord
\n
https://github.com/SWAT4HCLS/Biohackathon-SWAT4HCLS-2023/issues/4\nThis hack project is following up efforts of other to repurpose the Scholia platform for other SPARQL endpoints, like custom Wikibase installations or Wikidata subsets. In this project we will explore how we can make the Scholia code base configurable for the aspects to show, and which panels to show.\nIf the project is successful, we have a custom Scholia instance around any of the existing public SPARQL endpoints (e.g. ChEMBL, UniProt/NextProt, etc).
good morning. I am finishing some teaching before we start around 9am CET\nhacking ideas for this project include:
\n\n
global configurable SPARQL endpoint URL
\n
configurable subset of aspects to run
\n
mappings between Wikibase properties and classes with Wikidata equivalents (so that SPARQL can be in the \"Wikidata language\" but translated to the \"Wikibase language\" before being run)
\n
extract mapping of Wikidata classes (Q-ids) to Scholia aspects into a config file
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tz1ku4slulu9ib7intuj6bh.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tz1ku4slulu9ib7intuj6bh.json
new file mode 100644
index 0000000000..4685fae8f8
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/tz1ku4slulu9ib7intuj6bh.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"tz1ku4slulu9ib7intuj6bh","title":"Reading","desc":"","updated":1664198576882,"created":1664198508579,"custom":{},"fname":"ool.reading","type":"note","vault":{"fsPath":"vault"},"contentHash":"c3c142a97c35c18de00ecba3809f2f4d","links":[],"anchors":{"impossible-chemistry-may-reveal-origins-of-life-on-earth":{"type":"header","text":"'Impossible' chemistry may reveal origins of life on Earth","value":"impossible-chemistry-may-reveal-origins-of-life-on-earth","line":8,"column":0,"depth":1},"he-may-have-found-the-key-to-the-origins-of-life-so-why-have-so-few-heard-of-him":{"type":"header","text":"He may have found the key to the origins of life. So why have so few heard of him?","value":"he-may-have-found-the-key-to-the-origins-of-life-so-why-have-so-few-heard-of-him","line":12,"column":0,"depth":1}},"children":[],"parent":"2cxr093kvrg4jojokwgqrbj","data":{}},"body":"
Reading
\n
'Impossible' chemistry may reveal origins of life on Earth
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/u01xigvtf1bz7sbsua8hg4n.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/u01xigvtf1bz7sbsua8hg4n.json
new file mode 100644
index 0000000000..a2f97f4078
--- /dev/null
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..1bf433dcb8
--- /dev/null
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/uc53aopgkipjexmrmajuhte.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/uc53aopgkipjexmrmajuhte.json
new file mode 100644
index 0000000000..75322010dd
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This is Stephanie's daily open-notebook.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ugtv2j3wsqideeuqtatob3l.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ugtv2j3wsqideeuqtatob3l.json
new file mode 100644
index 0000000000..30d4cafe7c
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/ugtv2j3wsqideeuqtatob3l.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"ugtv2j3wsqideeuqtatob3l","title":"Ressources","desc":"","updated":1697022677545,"created":1693037661150,"custom":{},"fname":"projects.commons-public.microcosmics.ressources","type":"note","vault":{"fsPath":"vault"},"contentHash":"b24548f0ded942b19e04f9d7ec4b2a1d","links":[{"from":{"id":"aqe35lqv5khojyw2y5eottk","fname":"open-notebook.commons.pmallard.2023.09.28","vaultName":"vault"},"type":"backlink","position":{"start":{"line":22,"column":4,"offset":427},"end":{"line":22,"column":55,"offset":478},"indent":[]},"value":"projects.commons-public.microcosmics.ressources"}],"anchors":{},"children":[],"parent":"0zmqus0478ehzat7p16a7sr","data":{}},"body":"
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
\ No newline at end of file
diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/uqbtpj5ktfx07028x61rl9x.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/uqbtpj5ktfx07028x61rl9x.json
new file mode 100644
index 0000000000..3671a53de6
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/uqbtpj5ktfx07028x61rl9x.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"uqbtpj5ktfx07028x61rl9x","title":"Endpoint","desc":"","updated":1666553907133,"created":1666553880998,"custom":{},"fname":"lod.kg.endpoint","type":"note","vault":{"fsPath":"vault"},"contentHash":"b95f69202eb24f131f8dfdc5b120bd9b","links":[],"anchors":{"your-own-free-publicly-available-sparql-endpoint":{"type":"header","text":"Your own free, publicly available SPARQL endpoint","value":"your-own-free-publicly-available-sparql-endpoint","line":8,"column":0,"depth":1}},"children":[],"parent":"cm7lxhcj1gc5cubsyzd3811","data":{}},"body":"
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vDTgZL9UHWqYtBFdtD3vK.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vDTgZL9UHWqYtBFdtD3vK.json
new file mode 100644
index 0000000000..a6278c621a
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vDTgZL9UHWqYtBFdtD3vK.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"vDTgZL9UHWqYtBFdtD3vK","title":"Cfm","desc":"","updated":1635165794596,"created":1634199122481,"custom":{},"fname":"cfm","type":"note","vault":{"fsPath":"vault"},"contentHash":"858b292ba3030dbdf4bb44ee78793d59","links":[],"anchors":{},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
export RDBASE=~/Programs/rdkit-Release_2017_09_3/\n\n\nCMake Error: The following variables are used in this project, but they are set to NOTFOUND.\n
\n
Please set them or make sure they are set and tested correctly in the CMake files:\nINCHI_LIB (ADVANCED)\nlinked by target \"cfm-code\" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code\nRDINCHI_LIB (ADVANCED)\nlinked by target \"cfm-code\" in directory /home/allardpm/Programs/cfm-id-code/cfm/cfm-code
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vf9ewu2hzsbf7mx62vb5guz.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vf9ewu2hzsbf7mx62vb5guz.json
new file mode 100644
index 0000000000..995a23a48d
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vf9ewu2hzsbf7mx62vb5guz.json
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+{"pageProps":{"note":{"fname":"open-notebook.commons.mvisani","stub":true,"vault":{"fsPath":"vault"},"schemaStub":false,"type":"note","updated":1697541254231,"created":1697541254231,"id":"vf9ewu2hzsbf7mx62vb5guz","desc":"","links":[],"anchors":{},"children":["nmu1iz31fswfdevezly3un2"],"parent":"ne6ca7ufq0o7dqjc8q2ilnk","data":{},"title":"Mvisani"},"body":"
\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vhce2ufko0cuvj4peysipo9.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vhce2ufko0cuvj4peysipo9.json
new file mode 100644
index 0000000000..806a91e9f8
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vhce2ufko0cuvj4peysipo9.json
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+{"pageProps":{"note":{"id":"vhce2ufko0cuvj4peysipo9","title":"DNS","desc":"","updated":1654149429048,"created":1654149422219,"custom":{},"fname":"website.dns","type":"note","vault":{"fsPath":"vault"},"contentHash":"e51e1a6195291043ce32523efa3e791f","links":[],"anchors":{},"children":[],"parent":"wj0i9czxvt4v0b674nb8501","data":{}},"body":"
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vzowi0h8ykim61fcuo6gxu4.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/vzowi0h8ykim61fcuo6gxu4.json
new file mode 100644
index 0000000000..80dba9af13
--- /dev/null
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2023-05-12
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.05.12
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w4lyxdidjo3u07a0oifgkfl.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w4lyxdidjo3u07a0oifgkfl.json
new file mode 100644
index 0000000000..cf97d98bbd
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w4lyxdidjo3u07a0oifgkfl.json
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2023-03-22
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.22
\n
Notes
\n
Maëlle's presentation
\n
GNPS dashboard.
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w6xbnduraghd3i0zf9raell.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w6xbnduraghd3i0zf9raell.json
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i was not ble to kook the freeze dryer by myself. However I discussed with Edouard and we will do it together on wednesday.\nI have collected a total of 32 samples from the garden including 18 Acer species, 4 Citrus and 2 Ruta
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w75krbmkkvla3hwd66hn5bh.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w75krbmkkvla3hwd66hn5bh.json
new file mode 100644
index 0000000000..8fba722e2d
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w75krbmkkvla3hwd66hn5bh.json
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+{"pageProps":{"note":{"id":"w75krbmkkvla3hwd66hn5bh","title":"Pathway Analysis","desc":"","updated":1665848836340,"created":1663134554046,"custom":{},"fname":"pathway-analysis","type":"note","vault":{"fsPath":"vault"},"contentHash":"6ff3b90f6563ee30bb8aa96245902448","links":[],"anchors":{"ressources":{"type":"header","text":"Ressources","value":"ressources","line":14,"column":0,"depth":1},"omu":{"type":"header","text":"OMU","value":"omu","line":38,"column":0,"depth":2},"secimtools-a-suite-of-metabolomics-data-analysis-tools":{"type":"header","text":"SECIMTools: a suite of metabolomics data analysis tools","value":"secimtools-a-suite-of-metabolomics-data-analysis-tools","line":42,"column":0,"depth":2},"a-practical-guide-to-metabolomics-software-development":{"type":"header","text":"A Practical Guide to Metabolomics Software Development","value":"a-practical-guide-to-metabolomics-software-development","line":45,"column":0,"depth":2},"imap-a-web-server-for-metabolomics-data-integrative-analysis":{"type":"header","text":"iMAP: A Web Server for Metabolomics Data Integrative Analysis","value":"imap-a-web-server-for-metabolomics-data-integrative-analysis","line":48,"column":0,"depth":2}},"children":[],"parent":"QvYK9hGbCvPpEfSRYhV8j","data":{}},"body":"
Pathway Analysis
\n
Looking for scripts and approaches to perform pathway analysis on plants/bacterial metabolomics dataset
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w817k3pc4gq7qpa9jdox5u7.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w817k3pc4gq7qpa9jdox5u7.json
new file mode 100644
index 0000000000..1fbfd25d2c
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/w817k3pc4gq7qpa9jdox5u7.json
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+{"pageProps":{"note":{"id":"w817k3pc4gq7qpa9jdox5u7","title":"Test","desc":"","updated":1697022655659,"created":1697022634033,"custom":{},"fname":"projects.commons-public.microcosmics.rima.test","type":"note","vault":{"fsPath":"vault"},"contentHash":"26532fa6a9c182fa70adab04c80074a4","links":[],"anchors":{"titre":{"type":"header","text":"titre","value":"titre","line":11,"column":0,"depth":1},"sous-titre":{"type":"header","text":"sous titre","value":"sous-titre","line":13,"column":0,"depth":2},"resume":{"type":"header","text":"resume","value":"resume","line":24,"column":0,"depth":2}},"children":[],"parent":"tc1xx5yh5fqrzyo3lpltuqi","data":{}},"body":"
Test
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test rima
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titre
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sous titre
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fdjhfdjhfhd
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dshgdsgd
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/we641vahkb0idh203rsjzh2.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/we641vahkb0idh203rsjzh2.json
new file mode 100644
index 0000000000..c9638d0e72
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/we641vahkb0idh203rsjzh2.json
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on 17/03/2023 I orked with Eliane on the Agilent 1260 HC-DAD to develop a method to analyse the anacardiaceae samples. we took as a basis a method I previously used to analyse the leaves extracts of P. microcarpa. After several attempts we adopted the method below which gave rise to a better separation\n-T= 0 min 30% B 70% A\n-T= 1 min 30% B 70% A\n-T= 25 min 60 % B 40% A\n-T= 28 min 100% B 0% A\n-T= 33 Min 100% B 0% A\n-T= 38 min 30% B 70 % A for a Total run time 45 min\nwhere B is methanol containg 0.1 % TFA and A is water containing 0.1 % TFA. injection volume 10 Ul flow rate 0.2 mL/min DAD dectector at 360nm, 275 nm, 245 nm and 307 nm.
\n
\n
I have prepare the injection list for the batch odf sample to be analysed.
\n
Notes
\n
We used the method above to analyse pseudopondias samples 11 samples + seven pure compounds previously isolated from the leaves of Pseudospondias.
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..3eda90ae1e
--- /dev/null
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wl9UhkLI0rTQARpfVs77S.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wl9UhkLI0rTQARpfVs77S.json
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index 0000000000..e8b5a5b233
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wl9UhkLI0rTQARpfVs77S.json
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+{"pageProps":{"note":{"id":"wl9UhkLI0rTQARpfVs77S","title":"Scholia","desc":"","updated":1663407088677,"created":1614560154058,"custom":{},"fname":"wikidata.scholia","type":"note","vault":{"fsPath":"vault"},"contentHash":"48bbd83af7b5559d108181419a11525f","links":[],"anchors":{"scholia":{"type":"header","text":"Scholia","value":"scholia","line":10,"column":0,"depth":1},"interest-of-scholia-as-a-curation-page-for-lotus-data":{"type":"header","text":"Interest of Scholia as a curation page for LOTUS data","value":"interest-of-scholia-as-a-curation-page-for-lotus-data","line":18,"column":0,"depth":2},"contribution":{"type":"header","text":"Contribution","value":"contribution","line":25,"column":0,"depth":2},"egons-footnote":{"type":"header","text":"Egon's footnote","value":"egons-footnote","line":31,"column":0,"depth":2},"daniels-mail":{"type":"header","text":"Daniels mail","value":"daniels-mail","line":35,"column":0,"depth":2},"other-links":{"type":"header","text":"Other links","value":"other-links","line":67,"column":0,"depth":2},"scholia-search-examples":{"type":"header","text":"Scholia search examples","value":"scholia-search-examples","line":75,"column":0,"depth":2},"combined-topics":{"type":"header","text":"Combined topics","value":"combined-topics","line":76,"column":0,"depth":3}},"children":[],"parent":"59ftsVxFXXM9bB43vfKwK","data":{}},"body":"
Have you heard about Wikidata already? \"Use Scholia and Wikidata to find scientific literature\" is a new tutorial from my colleague Lauren Dupuis. https://laurendupuis.github.io/Scholia_tutorial/
With regards to forks, the most prominent example is probably\nhttps://ordia.toolforge.org/ ,\nwhich visualizes linguistic information based on the lexeme namespace in Wikidata.
adding additional SPARQL queries to existing Scholia pages is relatively straightforward (the main issue here is performance), so things like adding \"found in taxon\"-based queries to Scholia pages about compounds or taxa and perhaps also pathways could be solved quickly.
The work on such subaspects has been described in\nhttps://www.wikidata.org/wiki/Q50813856 for the example of geodata,\nwhich would probably be a good starting point when considering the effort involved.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wsndq74fuck4q6ivovplr64.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wsndq74fuck4q6ivovplr64.json
new file mode 100644
index 0000000000..fef940cb01
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wsndq74fuck4q6ivovplr64.json
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+{"pageProps":{"note":{"id":"wsndq74fuck4q6ivovplr64","title":"2023-04-13","desc":"","updated":1681404476056,"created":1681370401149,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.04.13","type":"note","vault":{"fsPath":"vault"},"contentHash":"f9eb9c25eda68f92db397fd05a14022d","links":[],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":18,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":19,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":21,"column":0,"depth":2},"metabolite-annotation-audrey-and-stephanie":{"type":"header","text":"Metabolite annotation Audrey and Stephanie","value":"metabolite-annotation-audrey-and-stephanie","line":23,"column":0,"depth":3},"paused":{"type":"header","text":"Paused","value":"paused","line":41,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":43,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":45,"column":0,"depth":2},"eclipta-alba":{"type":"header","text":"Eclipta alba","value":"eclipta-alba","line":58,"column":0,"depth":2},"c-forskohlii":{"type":"header","text":"C forskohlii","value":"c-forskohlii","line":78,"column":0,"depth":2},"conclusion":{"type":"header","text":"Conclusion","value":"conclusion","line":89,"column":0,"depth":3},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":107,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":110,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":111,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":114,"column":0,"depth":2}},"children":[],"parent":"itinl4oosihdr0r1gc1t929","data":{}},"body":"
2023-04-13
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.04.13
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
Q : why such difference in the raw extracts conc used for testing ?\nQ : can you explain the heatmap again ?\nQ : stats significative diff\nQ : how did you annotate the compounds ? Which software ? Which DB ?
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wxpuqu8009clfidfxuvp83n.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wxpuqu8009clfidfxuvp83n.json
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index 0000000000..40b528c8f3
--- /dev/null
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@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"wxpuqu8009clfidfxuvp83n","title":"09","desc":"","updated":1678358461031,"created":1678356204819,"custom":{},"fname":"meetings.group-meetings.2023.03.09","type":"note","vault":{"fsPath":"vault"},"contentHash":"33ee49d40ff9205b61d0bf94f4b9366f","links":[],"anchors":{"group-meeting-20230309":{"type":"header","text":"Group meeting 2023.03.09","value":"group-meeting-20230309","line":9,"column":0,"depth":1},"program":{"type":"header","text":"Program","value":"program","line":19,"column":0,"depth":1},"notes":{"type":"header","text":"Notes","value":"notes","line":28,"column":0,"depth":1},"marco":{"type":"header","text":"Marco","value":"marco","line":30,"column":0,"depth":2},"lëndita":{"type":"header","text":"Lëndita","value":"lëndita","line":34,"column":0,"depth":2},"pm":{"type":"header","text":"PM","value":"pm","line":40,"column":0,"depth":2}},"children":[],"parent":"x8xohlwatuwvaasq6tnejw4","data":{}},"body":"
09
\n
Group meeting 2023.03.09
\n
Present :
\n
\n
Lëndita
\n
Maëlle
\n
Marco
\n
PM
\n
Stéphanie
\n
\n
Program
\n
Short (from 10 - 20 min) presentation of everybody's project with some background
\n
\n
Maëlle
\n
Marco
\n
Lëndita
\n
Stéphanie
\n
\n
Notes
\n
Marco
\n
Told us :
\n
\n
never say that the probability is one !
\n
\n
Lëndita
\n
\n
Switch from the \"cutting\" pilot to testing the effects of repeated freeze-drying cycle.
Checked with everybody and Wednesday mornings should be OK.
\n
Check prices of :
\n
\n
lyophilisator
\n
1mg precision scale
\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wyghqjw6peta2vaci9d0fw6.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wyghqjw6peta2vaci9d0fw6.json
new file mode 100644
index 0000000000..1d5ff59480
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/wyghqjw6peta2vaci9d0fw6.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"wyghqjw6peta2vaci9d0fw6","title":"2023-08-22","desc":"","updated":1692722325972,"created":1692720332397,"traitIds":["open-notebook-commons-pmallard"],"custom":{},"fname":"open-notebook.commons.pmallard.2023.08.22","type":"note","vault":{"fsPath":"vault"},"contentHash":"6bb8a77180f0d8863e03a77b397600d8","links":[{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.08.22","id":"wyghqjw6peta2vaci9d0fw6","vaultName":"vault"},"value":"viewpoint","position":{"start":{"line":13,"column":5,"offset":285},"end":{"line":13,"column":18,"offset":298},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"viewpoint"}},{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.08.22","id":"wyghqjw6peta2vaci9d0fw6","vaultName":"vault"},"value":"people.rima-ouchene","position":{"start":{"line":21,"column":9,"offset":328},"end":{"line":21,"column":32,"offset":351},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"people.rima-ouchene"}},{"type":"wiki","from":{"fname":"open-notebook.commons.pmallard.2023.08.22","id":"wyghqjw6peta2vaci9d0fw6","vaultName":"vault"},"value":"project.microcosmics","position":{"start":{"line":25,"column":45,"offset":654},"end":{"line":25,"column":69,"offset":678},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"project.microcosmics"}}],"anchors":{"this-is-pmass-commons-lab-daily-open-notebook":{"type":"header","text":"This is PMAS's COMMONS Lab daily Open Notebook.","value":"this-is-pmass-commons-lab-daily-open-notebook","line":10,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":14,"column":0,"depth":2},"have-a-look-at-the-commons-research-discussion-forum":{"type":"header","text":"Have a look at the COMMONS research discussion forum","value":"have-a-look-at-the-commons-research-discussion-forum","line":16,"column":0,"depth":3},"daily-work-on-the-open-science-for-natural-products-research-viewpoint":{"type":"header","text":"Daily work on the Open Science for natural products research Viewpoint","value":"daily-work-on-the-open-science-for-natural-products-research-viewpoint","line":19,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":24,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":25,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":27,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":39,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":41,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":43,"column":0,"depth":2},"todo-tomorrow-one-day--or-never":{"type":"header","text":"Todo tomorrow, one day ... or never","value":"todo-tomorrow-one-day--or-never","line":45,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":48,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":49,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":52,"column":0,"depth":2}},"children":[],"parent":"rvqeqbxn9m3a62ibrbufszk","data":{}},"body":"
2023-08-22
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.08.22
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
Reading people.rima-ouchene (Private) proposition.\nRima will join the lab starting September for a 3 months internship. The idea was to work on the somewhat archived (for now) Mircocosmics projects.\nAnd for her to get familiar with open science and metabo/computational metabolomics approaches.
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/x8xohlwatuwvaasq6tnejw4.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/x8xohlwatuwvaasq6tnejw4.json
new file mode 100644
index 0000000000..5cf0002097
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/x8xohlwatuwvaasq6tnejw4.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/xczpb1ry8bv01ea6jfwcx12.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/xczpb1ry8bv01ea6jfwcx12.json
new file mode 100644
index 0000000000..716b78af49
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/xczpb1ry8bv01ea6jfwcx12.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"xczpb1ry8bv01ea6jfwcx12","title":"Luca","desc":"","updated":1664313870576,"created":1664313851416,"custom":{},"fname":"ool.luca","type":"note","vault":{"fsPath":"vault"},"contentHash":"9aa71baaaff448af94aa9afb8248322c","links":[],"anchors":{},"children":[],"parent":"2cxr093kvrg4jojokwgqrbj","data":{}},"body":"
Luca
\n
Last Universal Common Ancestor (LUCA)\nSome authors equate models of the origin of life with LUCA, the Last Universal Common Ancestor of all extant life.[17] This is a serious error resulting from failure to recognize that L refers to the last common ancestor, not to the first ancestor, which is much older: a large amount of evolution occurred before the appearance of LUCA.[18]
\n
Gill and Forterre expressed the essential point as follows:[19]
\n
LUCA should not be confused with the first cell, but was the product of a long period of evolution. Being the \"last\" means that LUCA was preceded by a long succession of older \"ancestors.\"
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/xfayuqwz8zd1ulxd8gv90yo.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/xfayuqwz8zd1ulxd8gv90yo.json
new file mode 100644
index 0000000000..2340f1574e
--- /dev/null
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2023-02-10
\n
This is Marco's daily open-notebook.
\n
Today is 2023.02.10
\n
Todo today
\n
Theory and ideas of the project
\n
We seek to infer the presence or absence of M metabolites in S species. We denote by xsm whether metabolite m=1,…,M is present (xsm=1) or absent (xsm=0) in species s=1,…,S. To infer the full vector x=(x11,…,x1M,…,xSM), we assume that related species share a similar set of metabolites and that metabolites related in their synthesis share a similar distribution across species.\nLet P(xsm=1∣ysm)=ysm be the probability with which metabolite m is present in species s. We then assume that
\n
logitysm=log1−ysmysm=μm+ϵsm
\n
where μ is a metabolite-specific intercept and ϵsm is normally distributed with mean 0 and co-variance cov(ϵsm,ϵs′m′)=ασss′+βσmm′ between each combination of species and metabolite. Here, σss′ and σmm′ are known measures of covariance between species s and s′ and between metabolites m and m′, respectively, and α and β are positive scalars.
\n
We consider two sets of data informative about x: i) Presence-absence data obtained with mass-spectrometry and ii) presence-only reports of specific metabolites in specific specie. Let dsj=(dsj1,…,dsjM) be the presence-absence vector of each metabolite m obtained with mass-spectrometry run j=1,…,Js performed on species s. Assuming a false-positive and false-negative error rates ϵ01 and ϵ10, respectively, we have
To model the presence only data, it must be put in relation to the expected research effort. Let psm denote the known number of presence-only reports for metabolite m in species s and nsm the unknown number of research projects that aimed at discovering metabolite m in species s. Assuming a false-positive and false-negative error rates π01 and π10, respectively, we have
\n
P(psm∣nsm,π01,π10)=...
\n
Product of cov ?! and not the sum ?
\n
Images
\n
Here are the first ideas of the discussion we had with Daniel and Pierre-Marie:
The probability of occurence of a given chemical class (i.e of a pseudo absence being indeed pseudo an not a real absence) could be formulated as the sum of probability of this occurence given the : chemical research effort context, phylogenetic context, covariance of other chemical classes.
\n
This last term was discussed: study of the covariance of chemical classes within a given taxa could be informative.
\n
\n
\n
Doing
\n
Paused
\n
Done
\n
Change prepare_pseudoabsence_tables.R in order to have a csv table and not a space separated data.
\n
Notes
\n
\"ref/noref, children/nochildren\" mean if you take into account multiple reference (and children) or not.
\n
So, for example: 2 articles report amarogentin in Gentiana lutea, 3 (of which 1 is the same) in Gentiana acaulis.
\n
Then, for the pair amarogentin in Gentiana:
\n
\n
ref_child : 5 → Gives the number of occurences were we find amarogentin related with a Gentiana species.
\n
ref_nochild: 4 → Gives how many different papers there are that talk about amarogentin in the species Gentiana
\n
noref_child : 2 → Gives how many children of that species were found with at least one reference (in that case : Gentiana \nlutea and Gentiana acaulis)
\n
noref_nochild: 1 → Will only be either 0 or 1. Gives if it there is at least one reference that talks about that molecule\nin the species Gentiana
\n
\n
ATTENTION tables are grouped also chemically. So child also refers to the \"chemical children\", so exactly same principle as for Gentiana and G. lutea but this for Terpenoids > Monoterpenoids > Secoiridoids (> Amarogentin)...
\n
Todo tomorrow
\n
\n
\n
\n
Today I learned that
\n
\n\n
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","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. 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In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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new file mode 100644
index 0000000000..8726cd5605
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yre279e7mgcr84ju3cn0ad5.json
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Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yu7xvrvcp8roccqaxcyp74j.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yu7xvrvcp8roccqaxcyp74j.json
new file mode 100644
index 0000000000..dc53d97b08
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yu7xvrvcp8roccqaxcyp74j.json
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from that paper they say that there is a lack of congruence between specialized chemistry and phylogeny may be caused by several different phenomena. One of them is convergent evolution. → we need to take this into account in our model.
\"Recent research on plant phylogeny coupled with metabolomics, which is the comprehensive analysis of metabolite profiles, has identified that related taxa produce similar secondary metabolites, although correlations are dependent also on environmental factors. \"
\n
interesting article stating that there is a need for creating a model such as what we are doing. We shouldn't forget to include environmental variable. It seems crucial.
\n
\n
\n
\n
Todo today
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. 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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yz6hq4xfzletlwqfvzsnqkl.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yz6hq4xfzletlwqfvzsnqkl.json
new file mode 100644
index 0000000000..fd9ad3a05b
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/yz6hq4xfzletlwqfvzsnqkl.json
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2023-03-05
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.03.05
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/z7qnncucq27a69shc7hge7p.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/z7qnncucq27a69shc7hge7p.json
new file mode 100644
index 0000000000..63bd9d8c2e
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/z7qnncucq27a69shc7hge7p.json
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+{"pageProps":{"note":{"id":"z7qnncucq27a69shc7hge7p","title":"Model","desc":"","updated":1691052461837,"created":1676306517796,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"projects.commons-public.anticipated-lotus.model","type":"note","vault":{"fsPath":"vault"},"contentHash":"7f783bb57790b746aba0d1c53b5b550a","links":[],"anchors":{"attention":{"type":"header","text":"ATTENTION","value":"attention","line":10,"column":0,"depth":1}},"children":[],"parent":"lzf7cyzlxb3t06ij206a8s4","data":{}},"body":"
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zc6n0kect0nyodshbvyon16.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zc6n0kect0nyodshbvyon16.json
new file mode 100644
index 0000000000..0d0b7ffe9a
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+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zc6n0kect0nyodshbvyon16.json
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+{"pageProps":{"note":{"id":"zc6n0kect0nyodshbvyon16","title":"2023-02-06","desc":"","updated":1675697249102,"created":1675677977641,"traitIds":["open-notebook-sguetchueng"],"custom":{},"fname":"open-notebook.commons.sguetchueng.2023.02.06","type":"note","vault":{"fsPath":"vault"},"contentHash":"fd2e54b3e784a05c12c9b3b593996e4c","links":[],"anchors":{"this-is-stephanies-daily-open-notebook":{"type":"header","text":"This is Stephanie's daily open-notebook.","value":"this-is-stephanies-daily-open-notebook","line":9,"column":0,"depth":1},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":13,"column":0,"depth":2},"have-a-look-at-the-dbgi-discussion-forum":{"type":"header","text":"Have a look at the DBGI discussion forum","value":"have-a-look-at-the-dbgi-discussion-forum","line":17,"column":0,"depth":3},"":{"type":"header","text":"","value":"","line":19,"column":0,"depth":3},"-1":{"type":"header","text":"","value":"-1","line":20,"column":0,"depth":3},"doing":{"type":"header","text":"Doing","value":"doing","line":22,"column":0,"depth":2},"paused":{"type":"header","text":"Paused","value":"paused","line":24,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":26,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":29,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":32,"column":0,"depth":2},"-2":{"type":"header","text":"","value":"-2","line":35,"column":0,"depth":3},"-3":{"type":"header","text":"","value":"-3","line":36,"column":0,"depth":3},"-4":{"type":"header","text":"","value":"-4","line":37,"column":0,"depth":3},"today-i-learned-that":{"type":"header","text":"Today I learned that","value":"today-i-learned-that","line":40,"column":0,"depth":2}},"children":[],"parent":"36354ldtt6g7yq3uvrjykle","data":{}},"body":"
2023-02-06
\n
This is Stephanie's daily open-notebook.
\n
Today is 2023.02.06
\n
Todo today
\n
extraction of plant sample using DBGI extraction Protocol\ncheck the metabolite profile of selected anacardiaceae\ndendron Tuto
extraction of plant sample with the help of Edouard\ndendron, VScodium tutorials with pierre Marie
\n
Notes
\n
\n\n
\n
Todo tomorrow
\n
Plant collection from the botanical garden and the processing prior to extraction\nworking on the malaria project
\n
\n
\n
\n
Today I learned that
\n
\n\n
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zj7mozg36lgdmvkyb01rw7i.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zj7mozg36lgdmvkyb01rw7i.json
new file mode 100644
index 0000000000..4678765a79
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/zj7mozg36lgdmvkyb01rw7i.json
@@ -0,0 +1 @@
+{"pageProps":{"note":{"id":"zj7mozg36lgdmvkyb01rw7i","title":"2023-03-09","desc":"","updated":1678373793759,"created":1678349461857,"traitIds":["open-notebook-mvisani"],"custom":{},"fname":"open-notebook.commons.mvisani.2023.03.09","type":"note","vault":{"fsPath":"vault"},"contentHash":"684e9bc5f2f8b79cada69b8555f42052","links":[],"anchors":{"this-is-marcos-daily-open-notebook":{"type":"header","text":"This is Marco's daily open-notebook.","value":"this-is-marcos-daily-open-notebook","line":9,"column":0,"depth":1},"women-in-data-science-geneva-event-2023":{"type":"header","text":"Women in Data Science Geneva event 2023","value":"women-in-data-science-geneva-event-2023","line":13,"column":0,"depth":2},"buidling-a-data-practice-from-scratch-for-cheap":{"type":"header","text":"Buidling a data practice from scratch for cheap","value":"buidling-a-data-practice-from-scratch-for-cheap","line":15,"column":0,"depth":3},"how-to-build-your-stack":{"type":"header","text":"How to build your stack","value":"how-to-build-your-stack","line":17,"column":0,"depth":4},"how-to-build-a-team":{"type":"header","text":"How to build a team","value":"how-to-build-a-team","line":26,"column":0,"depth":4},"graph-neural-networks":{"type":"header","text":"Graph neural networks","value":"graph-neural-networks","line":32,"column":0,"depth":3},"what-is-a-graph":{"type":"header","text":"What is a graph","value":"what-is-a-graph","line":35,"column":0,"depth":4},"what-are-they-for-":{"type":"header","text":"What are they for ?","value":"what-are-they-for-","line":40,"column":0,"depth":4},"how-to-implement-and-represent-a-graph-neural-network":{"type":"header","text":"How to implement and represent a graph neural network","value":"how-to-implement-and-represent-a-graph-neural-network","line":46,"column":0,"depth":4},"impact-":{"type":"header","text":"impact ?","value":"impact-","line":51,"column":0,"depth":4},"conclusion":{"type":"header","text":"Conclusion","value":"conclusion","line":57,"column":0,"depth":4},"lab-meeting-of-today":{"type":"header","text":"Lab meeting of today","value":"lab-meeting-of-today","line":63,"column":0,"depth":2},"notes":{"type":"header","text":"Notes","value":"notes","line":66,"column":0,"depth":2},"todo-today":{"type":"header","text":"Todo today","value":"todo-today","line":68,"column":0,"depth":2},"doing":{"type":"header","text":"Doing","value":"doing","line":71,"column":0,"depth":2},"done":{"type":"header","text":"Done","value":"done","line":74,"column":0,"depth":2},"todo-tomorrow":{"type":"header","text":"Todo tomorrow","value":"todo-tomorrow","line":78,"column":0,"depth":2}},"children":[],"parent":"oxbyb3iqmrqrlvwrlt40q4m","data":{}},"body":"
2023-03-09
\n
This is Marco's daily open-notebook.
\n
Today is 2023.03.09
\n
Women in Data Science Geneva event 2023
\n
\n
Buidling a data practice from scratch for cheap
\n
Christelle Marfaing, Head of Data, May
\n
How to build your stack
\n
\n
define and model your target \n
\n
Ingestion and processing frameworks
\n
technical monitoring
\n
data quality
\n
docs
\n
analysis tools
\n
\n
\n
build and model a road map
\n
\n
How to build a team
\n
\n
decentralize
\n
data mesh
\n
don't decentralize for nothing or reorganize all the time.
edge, link level : predict links between two nodes
\n
subgraph level: detect if nodes form a community (for ex: diagnostics)
\n
graph level : molecule property prediction for example
\n
\n
How to implement and represent a graph neural network
\n
\n
create adjacency matrix, or edge list, or adjacency list
\n
a graph can then be implemented into a feature matrix and adjacency matrix
\n
each node has to keep its own local information, take new information into account and update it's state based on the previous two.
\n
\n
impact ?
\n
example Google maps:
\n
\n
nodes: road segments
\n
edges : connectivity between road segments
\n
prediction: time of arrival
\n
\n
Conclusion
\n
\n
When ? Graph neural networks is a very powerful tool for complex and sparse data
\n
What for ? They can be successfully applied to a variety of different tasks such as node classification, graph classfication, edge prediction, etc...
\n
How ? We learned how to convert graph into ML read representation and build GNN
\n
\n
Lab meeting of today
\n
Notes
\n
Todo today
\n
\n\n
\n
Doing
\n
Done
\n
\n\n
\n
Todo tomorrow
","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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diff --git a/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/znidakc0zfvl32aqfgf4irf.json b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/znidakc0zfvl32aqfgf4irf.json
new file mode 100644
index 0000000000..174f9517db
--- /dev/null
+++ b/_next/data/DaEtwgAOeDfzWMALlWMKU/notes/znidakc0zfvl32aqfgf4irf.json
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\n","noteIndex":{"id":"QvYK9hGbCvPpEfSRYhV8j","title":"Welcome to the COMMONS Lab Open Dendron","desc":"","updated":1693056226815,"created":1630130450048,"custom":{"nav_order":0,"permalink":"/"},"fname":"root","type":"note","vault":{"fsPath":"vault"},"contentHash":"20f67df3dd870fc450a162c202c9ff41","links":[{"type":"wiki","from":{"fname":"root","id":"QvYK9hGbCvPpEfSRYhV8j","vaultName":"vault"},"value":"open-notebook.commons.setup","position":{"start":{"line":43,"column":118,"offset":1871},"end":{"line":43,"column":149,"offset":1902},"indent":[]},"xvault":false,"sameFile":false,"to":{"fname":"open-notebook.commons.setup"}}],"anchors":{"what-is-this-note":{"type":"header","text":"What is this note","value":"what-is-this-note","line":16,"column":0,"depth":2},"tutorial":{"type":"header","text":"Tutorial","value":"tutorial","line":20,"column":0,"depth":2},"dendron":{"type":"header","text":"Dendron.","value":"dendron","line":22,"column":0,"depth":3},"what-is-dendron-":{"type":"header","text":"What is Dendron ?","value":"what-is-dendron-","line":24,"column":0,"depth":4},"where-to-get-more-info-on-dendron-":{"type":"header","text":"Where to get more info on Dendron ?","value":"where-to-get-more-info-on-dendron-","line":30,"column":0,"depth":4},"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron":{"type":"header","text":"Concrete steps to access and contribute to the DBGI Dendron","value":"concrete-steps-to-access-and-contribute-to-the-dbgi-dendron","line":35,"column":0,"depth":4},"questions-comments-suggestions-":{"type":"header","text":"Questions, comments, suggestions ?","value":"questions-comments-suggestions-","line":52,"column":0,"depth":2}},"children":["e4ul30admmxm9ilxfq275cq","6ooxuf27zzf3grb14o18qf2","ih6vyup3yre4m9woc9ldl7k","vDTgZL9UHWqYtBFdtD3vK","jldFUSJGjDf1mFH8c2yUI","2rvdf4t5qnx5hqjj29bojcc","gvdyfgvq0z08fcfaqzmhtjo","46d1odkovrpdi6g16992phy","hpnaglyhnb48vuiniqecnqf","2cxr093kvrg4jojokwgqrbj","w75krbmkkvla3hwd66hn5bh","sk4m9gq7vz2t9phcxlxvqpw","43p60vv8btyhaclugl93jok","wj0i9czxvt4v0b674nb8501","ovslc641d0h00s16tf6kl8w","59ftsVxFXXM9bB43vfKwK","nmnpsy2e1rwqnqgurogi2u6","u01xigvtf1bz7sbsua8hg4n","p7c3qet5dgbd7gd012laax2","yre279e7mgcr84ju3cn0ad5","kj9v4h6p9gaypzlvdij6feg","blmlw21k1x22hqveca6nzde","500e30vbwe1wc5nky5wvoiw","r46x7sdh6q4btsy6mp62rkp"],"parent":null,"data":{},"body":"\n\n\nWelcome the the COMMONS Lab Open Dendron !\n\nIn the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.\n\nFor this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.\n\n## What is this note\n\nThis note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.\n\n## Tutorial\n\n### Dendron. \n\n#### What is Dendron ?\n\n> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.\n> \n> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.\n\n#### Where to get more info on Dendron ?\n\n- You can get more information in the Dendron system at the official website www.dendron.so\n- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.\n\n#### Concrete steps to access and contribute to the DBGI Dendron\n\n1. Install [VSCode](https://code.visualstudio.com/download)\n2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace \n3. Clone the COMMONS Dendron repo\n\n In your terminal\n ```\n git clone https://github.com/commons-research/commons-dws-public.git\n ```\n4. In VSCode open (File/Open) the cloned repository.\n5. Voila ! You should now be in the COMMONS Lab Open Dendron.\n\nFeel free to explore and contribute.\nA first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]\n\n\n## Questions, comments, suggestions ?\n\nFeel free to contribute here https://github.com/orgs/commons-research/discussions\n\n"},"collectionChildren":null,"customHeadContent":null,"config":{"version":5,"dev":{"enablePreviewV2":true},"commands":{"lookup":{"note":{"selectionMode":"extract","confirmVaultOnCreate":false,"leaveTrace":false,"bubbleUpCreateNew":true,"vaultSelectionModeOnCreate":"smart","fuzzThreshold":0.2}},"insertNote":{"initialValue":"templates"},"insertNoteLink":{"aliasMode":"none","enableMultiSelect":false},"insertNoteIndex":{"enableMarker":false},"randomNote":{},"copyNoteLink":{"aliasMode":"title"},"templateHierarchy":"template"},"workspace":{"vaults":[{"fsPath":"vault"}],"journal":{"dailyDomain":"daily","name":"journal","dateFormat":"y.MM.dd","addBehavior":"childOfDomain"},"scratch":{"name":"scratch","dateFormat":"y.MM.dd.HHmmss","addBehavior":"asOwnDomain"},"graph":{"zoomSpeed":1,"createStub":false},"enableAutoCreateOnDefinition":false,"enableXVaultWikiLink":false,"enableRemoteVaultInit":true,"workspaceVaultSyncMode":"noCommit","enableAutoFoldFrontmatter":false,"maxPreviewsCached":10,"maxNoteLength":204800,"task":{"name":"","dateFormat":"","addBehavior":"childOfCurrent","statusSymbols":{"":" ","wip":"w","done":"x","assigned":"a","moved":"m","blocked":"b","delegated":"l","dropped":"d","pending":"y"},"prioritySymbols":{"H":"high","M":"medium","L":"low"},"todoIntegration":false,"createTaskSelectionType":"selection2link","taskCompleteStatus":["done","x"]},"enableUserTags":true,"enableHashTags":true,"dendronVersion":"0.112.0","enableEditorDecorations":true,"enableFullHierarchyNoteTitle":false},"preview":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"automaticallyShowPreview":false,"enableFrontmatterTags":true,"enableHashesForFMTags":false},"publishing":{"enableFMTitle":true,"enableNoteTitleForLink":true,"enableMermaid":true,"enablePrettyRefs":true,"enableKatex":true,"assetsPrefix":"/commons-dws-public","copyAssets":true,"siteHierarchies":["root"],"enableSiteLastModified":true,"siteRootDir":"docs","siteUrl":"https://commons-research.github.io","enableFrontmatterTags":true,"enableHashesForFMTags":false,"enableRandomlyColoredTags":true,"duplicateNoteBehavior":{"action":"useVault","payload":["vault"]},"writeStubs":false,"seo":{"title":"COMMONS DWS Public","description":"Personal knowledge space"},"github":{"enableEditLink":true,"editLinkText":"Click here to edit this page on Github !","editBranch":"main","editViewMode":"edit","editRepository":"https://github.com/commons-research/commons-dws-public"},"enablePrettyLinks":true,"enableTaskNotes":true,"siteFaviconPath":"favicon.ico","siteIndex":"root","searchMode":"lookup"}}},"__N_SSG":true}
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@@ -0,0 +1 @@
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2023-06-24
\n
This is PMAS's COMMONS Lab daily Open Notebook.
\n
Today is 2023.06.24
\n
Todo today
\n
Have a look at the COMMONS research discussion forum
![](\"/commons-dws-public/assets/images/allard-lab.jpg\")
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]]\n[[![\"Alt](\"/commons-dws-public/image-6.png\")
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]]\n![](\"/commons-dws-public/assets/images/2023-10-12-10-01-08.png\")
\n![](\"/commons-dws-public/assets/images/2023-10-12-10-01-36.png\")
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]]\n[[![\"Alt](\"/commons-dws-public/image-2.png\")
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]]![](\"/commons-dws-public/assets/images/2023-10-12-09-58-57.png\")
\n![](\"/commons-dws-public/assets/images/2023-10-12-09-59-28.png\")
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pallette![](\"/commons-dws-public/assets/images/2023-10-12-09-19-51.png\")
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