From f9ba8d0f1f8e12231e89b6ffee65ec1adc8ba5dc Mon Sep 17 00:00:00 2001 From: Patrick Capon <137233925+PatCapon39@users.noreply.github.com> Date: Tue, 17 Dec 2024 13:39:50 +1000 Subject: [PATCH] Add structural biology collection (#15) * Update table_conversion.py * Update resource-table-all.html * update library * Wording change in jobs for update_library.yml * change all references to 'tools' to 'resources' * Remove code related to countries * Create structural_biology.md * Delete _data/tool_and_resource_list.yml * Delete _data/full_resource_list.yml * Update topnav.yml * Add structural biology to navigation pane * update library * Update main.yml fix syntax * Update resource-table-all.html * Update table_conversion.py * update library * Update topnav.yml --------- Co-authored-by: GitHub Action --- .github/workflows/update_library.yml | 2 +- ...resource_list.yml => all_content_list.yml} | 378 ++++++++++++++---- _data/full_resource_list.yml | 269 ------------- _data/sidebars/main.yml | 2 + _data/topnav.yml | 8 +- _includes/resource-table-all.html | 38 +- pages/structural_biology.md | 12 + scripts/table_conversion.py | 16 +- 8 files changed, 341 insertions(+), 384 deletions(-) rename _data/{tool_and_resource_list.yml => all_content_list.yml} (55%) delete mode 100644 _data/full_resource_list.yml create mode 100644 pages/structural_biology.md diff --git a/.github/workflows/update_library.yml b/.github/workflows/update_library.yml index b69b36e..07bbb43 100644 --- a/.github/workflows/update_library.yml +++ b/.github/workflows/update_library.yml @@ -9,7 +9,7 @@ on: jobs: - update_guides: + update_library: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 diff --git a/_data/tool_and_resource_list.yml b/_data/all_content_list.yml similarity index 55% rename from _data/tool_and_resource_list.yml rename to _data/all_content_list.yml index 85c06de..10471c1 100644 --- a/_data/tool_and_resource_list.yml +++ b/_data/all_content_list.yml @@ -1,133 +1,134 @@ -- Topics: Proteomics, Data sharing +- collection: + - data_management description: 'A tutorial with an overview of PRoteomics IDEntification (PRIDE) database, how to search and download datasets from PRIDE and an introduction of PRIDE tools: Proteome Xchange Submission Tool and PRIDE Inspector (to assess the quality of a dataset). ' name: PRIDE - Quick tour provider: EMBL-EBI - related_pages: - - data_management + topics: Proteomics, Data sharing type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/ -- Topics: Data sharing, Proteomics +- collection: + - data_management description: A webinar covering proteomics data submission process including a demo for Proteome Xchange Submission Tool. name: 'PRIDE database: Proteomics data submission, access and visualisation' provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Proteomics type: Webinar url: https://www.ebi.ac.uk/training/events/pride-database-proteomics-data-submission-access-and-visualisation/ -- Topics: Data collection, Data reuse, Proteomics +- collection: + - data_management description: 'A webinar with an introduction to the proteomes and how to find and download relevant protein datasets. It also includes a UniProt demonstration to find proteomic data with user queries. ' name: Understanding Proteomes provider: EMBL-EBI - related_pages: - - data_management + topics: Data collection, Data reuse, Proteomics type: Webinar url: https://www.ebi.ac.uk/training/events/understanding-proteomes/ -- Topics: Data sharing, Metagenomics +- collection: + - data_management description: 'A webinar with an introduction of ENA, INSDC agreement, the ENA data and metadata model, how to structure a metagenomic study and submit metagenomics data to ENA. ' name: Submitting metagenomic data to ENA provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Metagenomics type: Webinar url: https://www.ebi.ac.uk/training/events/submitting-metagenomic-data-ena/ -- Topics: Data analysis, Data reuse, Metagenomics +- collection: + - data_management description: 'A workshop covering how to search and retrieve and perform analysis on metagenomic sequencing data from NCBI ' name: An NCBI Guide to Finding and Analyzing Metagenomic Data provider: NCBI - related_pages: - - data_management + topics: Data analysis, Data reuse, Metagenomics type: Workshop url: https://www.nlm.nih.gov/ncbi/workshops/2022-10_Guide-to-Metagenomics/workshop-details.html -- Topics: Data sharing, Metagenomics +- collection: + - data_management description: A tutorial with a detailed walkthrough for submitting metagenomics data to ENA for analysis by MGnify, highlighting metadata standardization, the use of templates like GSC MIxS for contextual information, and submission methods through ENA or the MGnify browser name: MGnify portal - Submitting metagenomics data to the European Nucleotide Archive provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Metagenomics type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/mgnify-portal/ -- Topics: Data sharing, Metabolomics +- collection: + - data_management description: A tutorial offering an introduction to Metabolights, a summary of data submission and retrieval processes, along with additional support resources. name: Metabolights - Quick Tour provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Metabolomics type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/metabolights-quick-tour/ -- Topics: Data sharing, Metabolomics +- collection: + - data_management description: A webinar introducing MetaboLights, metabolomics, and the Metabolomics Standards Initiative (MSI), demonstrating how to navigate the MetaboLights site to explore study information and providing a brief overview of study submission. name: 'MetaboLights: the home for metabolomics experiments and derived information' provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Metabolomics type: Webinar url: https://www.ebi.ac.uk/training/events/metabolights-home-metabolomics-experiments-and-derived-information/ -- Topics: Data planning +- collection: + - data_management description: A webinar about open access data, examples of making BioSamples submissions FAIR, open data at IntAct database and how PMC Europe is promoting open access publicationg name: 'Open with purpose: How and why to make your data open' provider: EMBL-EBI - related_pages: - - data_management + topics: Data planning type: Webinar url: https://www.ebi.ac.uk/training/events/open-purpose-how-and-why-make-your-data-open/ -- Topics: Data collection, data reuse +- collection: + - data_management description: A tutorial about publicly available data and importance of licenses to make the data open. Topics covered include data formats, controlled vocabularies, ontologies, reporting guidelines, minimum reporting checklists and importance of unique identifiers for data artefacts. name: Using Publicly available data provider: EMBL-EBI - related_pages: - - data_management + topics: Data collection, data reuse type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/using-publicly-available-data/ -- description: 'A tutorial encompassing concepts of data management e.g. the data +- collection: + - data_management + description: 'A tutorial encompassing concepts of data management e.g. the data management cycle, data management tools (DMPonline and Data stewardship wizard), FAIRness vs Openness, benefits/challenges of data sharing, and ontologies/standards (e.g. The Ontology Lookup Service (OLS) and The Experimental Factor Ontology (EFO)) to be used to describe/annotate data. ' name: Bringing data to life, Data management for the biomolecular sciences provider: EMBL-EBI - related_pages: - - data_management type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/bringing-data-to-life-data-management/ -- Topics: Data sharing +- collection: + - data_management description: 'A webinar with discussion regarding importance of sharing research data and infrastructure available at EMBL-EBI to support sharing. It also describes data submission process to IntAct and ComplexPortal. ' name: 'Open access: Data sharing and submission' provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing type: Webinar url: https://www.ebi.ac.uk/training/events/open-access-data-sharing-and-submission/ -- Topics: Data sharing +- collection: + - data_management description: A webinar covering processes of data retrieval and submission to BioStudies. name: A guide to organising data associated to a publication using BioStudies provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing type: Webinar url: https://www.ebi.ac.uk/training/events/guide-organising-data-associated-publication-using-biostudies/ -- Topics: Data collection, data reuse +- collection: + - data_management description: ' @@ -137,58 +138,58 @@ name: An Introduction to Accessing NCBI Resources on the Command Line using EDirect for Biologists provider: NCBI - related_pages: - - data_management + topics: Data collection, data reuse type: Workshop url: https://ncbiinsights.ncbi.nlm.nih.gov/event/command-line-03-2023/ -- Topics: Data collection, Data reuse, Data analysis +- collection: + - data_management description: 'A workshop demonstrating effective use of python programming, BioPython package and Jupyter notebooks to facilitate download, analysis and visualisation of data in a reproducible fashion. ' name: Getting Started with NCBI Data in Python provider: NCBI - related_pages: - - data_management + topics: Data collection, Data reuse, Data analysis type: Workshop url: https://ncbiinsights.ncbi.nlm.nih.gov/event/getting-started-with-ncbi-data-in-python-04-22/ -- Topics: Data sharing +- collection: + - data_management description: A tutorial introducing the BioSamples database and the concept of a biosample. It also provides website navigation tips, and directs users to more information on accessing and downloading data from BioSamples. name: BioSamples Quick tour provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/biosamples-quick-tour/ -- Topics: Data planning, Data sharing +- collection: + - data_management description: What metadata is and why it is important to keep track of this information in biological experiments. name: Describing data consistently provider: EMBL-EBI - related_pages: - - data_management + topics: Data planning, Data sharing type: Short Video url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/what-makes-a-good-bioinformatics-database/describing-data-consistently/ -- Topics: Data planning +- collection: + - data_management description: Basic tips on managing and sharing data to maximise its re-use in the future. name: Tips on managing and sharing data provider: EMBL-EBI - related_pages: - - data_management + topics: Data planning type: Guide url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/tips-on-managing-and-sharing-data/ -- Topics: Data planning, Genomics +- collection: + - data_management description: These slides focus on topics such as discipline-specific repositories, generalist repositories, the FAIRDOM platform, and reproducible models in FAIRDOM. name: Data publishing and archival provider: ELIXIR Luxembourg - related_pages: - - data_management + topics: Data planning, Genomics type: Slides url: https://zenodo.org/record/5524794 -- Topics: Data collection, Data reuse, Data analysis, Genomics +- collection: + - data_management description: ' A workshop covering how to use AWS services like Athena to mine metadata from @@ -197,72 +198,289 @@ application.' name: An Introduction to NCBI Cloud Computing for Biologists provider: NCBI - related_pages: - - data_management + topics: Data collection, Data reuse, Data analysis, Genomics type: Workshop url: https://www.nlm.nih.gov/oet/ed/ncbi/2022_07_cloud.html -- Topics: Data sharing, Genomics +- collection: + - data_management description: A tutorial covering the importance of data submission, metadata templates like MIAME and MINSEQE, submission timelines, and submission locations for functional genomics data (e.g. ArrayExpress and GEO). It also discusses secondary databases like Expression Atlas. name: Functional Genomics - Submitting data provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Genomics type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/functional-genomics-iii-submitting-data/ -- Topics: Data planning, Genomics +- collection: + - data_management description: A webinar offering an overview of EGA, discussing its controlled access data, the process for gaining access through the Data Access Committee, the use of DUO ontology for tagging data, and a live demo of pyEGA3 for downloading permitted data. name: Introduction to exploring genome-phenome data with EGA provider: EMBL-EBI - related_pages: - - data_management + topics: Data planning, Genomics type: Webinar url: https://www.ebi.ac.uk/training/events/introduction-exploring-genome-phenome-data-ega/ -- Topics: Data sharing +- collection: + - data_management description: A webinar offering a detailed guide on submitting data to the GWAS Catalog, including user account setup, data format conversion, metadata provision, and validation using a command-line tool, with an emphasis on explaining metadata columns. name: Submitting your genome wide association study data to the GWAS Catalog provider: EMBL-EBI - related_pages: - - genomics - - data_management + topics: Data sharing, Genomics type: Webinar url: https://www.ebi.ac.uk/training/events/submitting-your-genome-wide-association-study-data-gwas-catalog/ -- Topics: Data collection, Data reuse, Data sharing +- collection: + - data_management description: A webinar introducing the background of the European Nucleotide Archive (ENA), data and metadata models, submission and retrieval processes, submission methods, and tools for data download. name: Nucleotide sequencing data submission and retrieval at the ENA provider: EMBL-EBI - related_pages: - - genomics - - data_management + topics: Data collection, Data reuse, Data sharing, Genomics type: Webinar url: https://www.ebi.ac.uk/training/events/nucleotide-sequencing-data-submission-and-retrieval-ena/ -- Topics: Data sharing, Data reuse +- collection: + - data_management description: A webinar providing an overview of the European Variation Archive (EVA) and its integration with other EBI resources, a live demo of the EVA interface for accessing data via web, FTP, or API, and clarification on using SS and RS IDs for variant access/reference. name: Variant submission and data access at the European Variation Archive provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing, Data reuse type: Webinar url: https://www.ebi.ac.uk/training/events/variant-submission-and-data-access-european-variation-archive/ -- Topics: Data sharing +- collection: + - data_management description: 'A tutorial introducing ArrayExpress and describing Annotare tool and MAGE-TAB spreadsheet method for data submission. ' name: ArrayExpress in BioStudies provider: EMBL-EBI - related_pages: - - data_management + topics: Data sharing type: Online tutorial url: https://www.ebi.ac.uk/training/online/courses/arrayexpress-in-biostudies/#vf-tabs__section--overview +- collection: + - structural_biology + description: The best way to get up to competency with using an interpreting AlphaFold. + Should be done by all grad students using AF + name: EMBL-EBI AlphaFold Guide + provider: EMBL-EBI + topics: Structure prediction + type: Online tutorial + url: https://www.ebi.ac.uk/training/online/courses/alphafold/ +- collection: + - structural_biology + description: A visual walkthrough of the AlphaFold3 architecture, with more details + and diagrams than you were probably looking for. + name: AlphaFold3 explainer + provider: Community member + topics: Structure prediction + type: Guide + url: https://elanapearl.github.io/blog/2024/the-illustrated-alphafold/ +- collection: + - structural_biology + description: Lists state-of-the-art and emerging tools for Biomolecular Structure + Prediction. + name: Biomolecular Structure Prediction Tools + provider: Community member + topics: Structure prediction + type: Guide + url: https://abeebyekeen.com/biomodes-biomolecular-structure-prediction/ +- collection: + - structural_biology + description: User guide for running MMseqs from the command line + name: MMseqs2 tutorial + provider: Community member + type: Guide + url: https://github.com/soedinglab/MMseqs2/wiki/Tutorials +- collection: + - structural_biology + description: User guide for running Hiden Markov Models of protein sequences on + the command line + name: HH-suite tutorial + provider: Community member + type: Guide + url: https://github.com/soedinglab/hh-suite/wiki +- collection: + - structural_biology + description: User guide for running HMMER on the command line + name: HMMER tutorial + provider: Community member + type: Guide + url: http://hmmer.org/documentation.html +- collection: + - structural_biology + description: Walkthrough guide on running RFDiffusion + name: RFDiffusion + provider: Community member + type: Guide + url: https://github.com/RosettaCommons/RFdiffusion +- collection: + - structural_biology + description: User guide on protein design with Rosetta + name: Rosetta tutorial + provider: Community member + type: Guide + url: https://docs.rosettacommons.org/docs/latest/Home +- collection: + - structural_biology + description: Collection of how-to guides for protein design + name: Pyrosetta tutorials + provider: Community member + type: Guide + url: https://github.com/ProteinDesignLab/protein-design-tutorials +- collection: + - structural_biology + description: Google Colab notebooks for running protein design + name: ColabDesign notebooks + provider: Community member + type: Guide + url: https://github.com/sokrypton/ColabDesign +- collection: + - structural_biology + description: Molecular Dynamics simulation tutorials + name: GROMACS tutorials + provider: Community member + topics: Molecular dynamics + type: Guide + url: http://www.mdtutorials.com/gmx/ +- collection: + - structural_biology + description: Molecular Dynamics simulation tutorials + name: GROMACS tutorials + provider: Community member + topics: Molecular dynamics + type: Guide + url: https://gromacstutorials.github.io/ +- collection: + - structural_biology + description: Molecular Dynamics simulation tutorials + name: LAMMPS tutorials + provider: Community member + topics: Molecular dynamics + type: Guide + url: https://lammpstutorials.github.io/ +- collection: + - structural_biology + description: Molecular Dynamics simulation tutorials + name: Amber tutorial + provider: Community member + topics: Molecular dynamics + type: Guide + url: https://ambermd.org/tutorials/ +- collection: + - structural_biology + description: Short how-to guide on using BLAST from the command line + name: BLAST tutorial + provider: tinybio + type: Guide + url: https://docs.tinybio.cloud/docs/blast-tutorial +- collection: + - structural_biology + description: Three short tutorials for running ColabFold + name: ColabFold tutorial + provider: Community member + topics: Structure prediction + type: Guide + url: https://protocolexchange.researchsquare.com/article/pex-2490/v1 +- collection: + - structural_biology + description: Covers basics of ssh and jupyter notebooks on a HPC + name: Running ColabFold notebook on a HPC + provider: Community member + type: Guide + url: https://www.jameslingford.com/blog/colabfold-hpc-ssh-howto/ +- collection: + - structural_biology + description: Protein visualisation guides for UCSF ChimeraX + name: ChimeraX recipes + provider: Community member + topics: Protein visualisation + type: Guide + url: https://rbvi.github.io/chimerax-recipes/ +- collection: + - structural_biology + description: ChimeraX how-to + name: ChimeraX cavity visualisation + provider: Community member + type: Guide + url: https://www.jameslingford.com/blog/chimerax-cavity-surfaces/ +- collection: + - structural_biology + description: ChimeraX how-to + name: ChimeraX outline selected area + provider: Community member + type: Guide + url: https://www.jameslingford.com/blog/chimerax-outlines/ +- collection: + - structural_biology + description: ~1hr talks by method developers on recent breakthroughs in protein + modelling + name: Boston Protein Design and Modeling Club + provider: Community member + type: Webinar + url: https://www.youtube.com/@bpdmc +- collection: + - structural_biology + description: 100 second videos on how to use various protein tools. Guides are with + their clean proprietary interface + name: NeuroSnap protein design videos + provider: Community member + type: Short Video + url: https://www.youtube.com/@NeurosnapInc/videos +- collection: + - structural_biology + description: Talks focused on CryoEM but also computational structural biology and + protein design + name: Structural Biology Grid Consortium Talk Series + provider: Community member + type: Short Video + url: https://www.youtube.com/@SBGridTV/videos +- collection: + - structural_biology + description: Overview of the AlphaFold pipeline by the New England Journal of Medicine + name: AlphaFold 5 minute explainer - Medical Journal + provider: NEJM + type: Short Video + url: https://www.youtube.com/watch?v=7q8Uw3rmXyE +- collection: + - structural_biology + description: Detailed and lucid talk on understanding the machine learning concepts + behind AI protein structure prediction methods + name: ' AlphaFold2, OpenFold, Protein Language Models and Beyond | Nazim Bouatta ' + provider: Community member + type: Short Video + url: https://youtu.be/ON1ltprZKPo?si=WkZ3Y8eZfVusWUvo +- collection: + - structural_biology + description: Blender tutorials for protein animations + name: Brady Johnston Blender tutorials + provider: Community member + type: Short Video + url: https://www.youtube.com/@BradyJohnston +- collection: + - structural_biology + description: Blender tutorials for protein animations + name: Luminous Lab Blender tutorials + provider: Community member + type: Short Video + url: https://www.youtube.com/@LuminousLab +- collection: + - structural_biology + description: Playlist of tutorials on how to use ChimeraX with command lines + name: ChimeraX tutorials + provider: Community member + type: Short Video + url: https://youtube.com/playlist?list=PL4eF1KHNgDfIYSKCS3_S0PTRYtYTV9Myi&si=gBWxBbzifFmF32ln +- collection: + - structural_biology + description: Talks focused on molecular dynamics simulations and computational chemistry + name: European Centre of Excellence for Computational Biomolecular Research + provider: Community member + type: Short Video + url: https://youtube.com/@bioexcelcoe?si=5jSzsDzpBKwGQThr diff --git a/_data/full_resource_list.yml b/_data/full_resource_list.yml deleted file mode 100644 index a6bd9b7..0000000 --- a/_data/full_resource_list.yml +++ /dev/null @@ -1,269 +0,0 @@ -- description: 'A tutorial with an overview of PRoteomics IDEntification (PRIDE) database, - how to search and download datasets from PRIDE and an introduction of PRIDE tools: - Proteome Xchange Submission Tool and PRIDE Inspector (to assess the quality of - a dataset). ' - name: PRIDE - Quick tour - provider: EMBL-EBI - topics: - - Proteomics - - Data Sharing - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/pride-quick-tour/submitting-data-to-pride/ -- description: A webinar covering proteomics data submission process including a demo - for Proteome Xchange Submission Tool. - name: 'PRIDE database: Proteomics data submission, access and visualisation' - provider: EMBL-EBI - topics: - - Proteomics - - Data Sharing - type: Webinar - url: https://www.ebi.ac.uk/training/events/pride-database-proteomics-data-submission-access-and-visualisation/ -- description: 'A webinar with an introduction to the proteomes and how to find and - download relevant protein datasets. It also includes a UniProt demonstration to - find proteomic data with user queries. ' - name: Understanding Proteomes - provider: EMBL-EBI - topics: - - Proteomics - - Data Collection - - Data Reuse - type: Webinar - url: https://www.ebi.ac.uk/training/events/understanding-proteomes/ -- description: 'A webinar with an introduction of ENA, INSDC agreement, the ENA data - and metadata model, how to structure a metagenomic study and submit metagenomics - data to ENA. ' - name: Submitting metagenomic data to ENA - provider: EMBL-EBI - topics: - - Metagenomics - - 'Data Sharing ' - type: Webinar - url: https://www.ebi.ac.uk/training/events/submitting-metagenomic-data-ena/ -- description: 'A workshop covering how to search and retrieve and perform analysis - on metagenomic sequencing data from NCBI ' - name: An NCBI Guide to Finding and Analyzing Metagenomic Data - provider: NCBI - topics: - - Metagenomics - - Data Analysis - - Data Reuse - type: Workshop - url: https://www.nlm.nih.gov/ncbi/workshops/2022-10_Guide-to-Metagenomics/workshop-details.html -- description: A tutorial with a detailed walkthrough for submitting metagenomics - data to ENA for analysis by MGnify, highlighting metadata standardization, the - use of templates like GSC MIxS for contextual information, and submission methods - through ENA or the MGnify browser - name: MGnify portal - Submitting metagenomics data to the European Nucleotide Archive - provider: EMBL-EBI - topics: - - Metagenomics - - 'Data Sharing ' - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/mgnify-portal/ -- description: A tutorial offering an introduction to Metabolights, a summary of data - submission and retrieval processes, along with additional support resources. - name: Metabolights - Quick Tour - provider: EMBL-EBI - topics: - - Metabolomics - - Data Sharing - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/metabolights-quick-tour/ -- description: A webinar introducing MetaboLights, metabolomics, and the Metabolomics - Standards Initiative (MSI), demonstrating how to navigate the MetaboLights site - to explore study information and providing a brief overview of study submission. - name: 'MetaboLights: the home for metabolomics experiments and derived information' - provider: EMBL-EBI - topics: - - Metabolomics - - Data Sharing - type: Webinar - url: https://www.ebi.ac.uk/training/events/metabolights-home-metabolomics-experiments-and-derived-information/ -- description: A webinar about open access data, examples of making BioSamples submissions - FAIR, open data at IntAct database and how PMC Europe is promoting open access - publicationg - name: 'Open with purpose: How and why to make your data open' - provider: EMBL-EBI - topics: - - Data Planning - type: Webinar - url: https://www.ebi.ac.uk/training/events/open-purpose-how-and-why-make-your-data-open/ -- description: A tutorial about publicly available data and importance of licenses - to make the data open. Topics covered include data formats, controlled vocabularies, - ontologies, reporting guidelines, minimum reporting checklists and importance - of unique identifiers for data artefacts. - name: Using Publicly available data - provider: EMBL-EBI - topics: - - Data Collection - - Data Reuse - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/using-publicly-available-data/ -- description: 'A tutorial encompassing concepts of data management e.g. the data - management cycle, data management tools (DMPonline and Data stewardship wizard), - FAIRness vs Openness, benefits/challenges of data sharing, and ontologies/standards - (e.g. The Ontology Lookup Service (OLS) and The Experimental Factor Ontology (EFO)) - to be used to describe/annotate data. ' - name: Bringing data to life, Data management for the biomolecular sciences - provider: EMBL-EBI - topics: - - Data Planning - - Data Sharing - - Data Reuse - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/bringing-data-to-life-data-management/ -- description: 'A webinar with discussion regarding importance of sharing research - data and infrastructure available at EMBL-EBI to support sharing. It also describes - data submission process to IntAct and ComplexPortal. ' - name: 'Open access: Data sharing and submission' - provider: EMBL-EBI - topics: - - Data Sharing - type: Webinar - url: https://www.ebi.ac.uk/training/events/open-access-data-sharing-and-submission/ -- description: A webinar covering processes of data retrieval and submission to BioStudies. - name: A guide to organising data associated to a publication using BioStudies - provider: EMBL-EBI - topics: - - Data Sharing - type: Webinar - url: https://www.ebi.ac.uk/training/events/guide-organising-data-associated-publication-using-biostudies/ -- description: ' - - - A workshop teaching biological researchers how to use the command line to search - and fetch NCBI data, focusing on creating bash commands to download and organize - files and constructing search queries with the EDirect toolkit' - name: An Introduction to Accessing NCBI Resources on the Command Line using EDirect - for Biologists - provider: NCBI - topics: - - Data Collection - - Data Reuse - type: Workshop - url: https://ncbiinsights.ncbi.nlm.nih.gov/event/command-line-03-2023/ -- description: 'A workshop demonstrating effective use of python programming, BioPython - package and Jupyter notebooks to facilitate download, analysis and visualisation - of data in a reproducible fashion. ' - name: Getting Started with NCBI Data in Python - provider: NCBI - topics: - - Data Collection - - Data Analysis - - Data Reuse - type: Workshop - url: https://ncbiinsights.ncbi.nlm.nih.gov/event/getting-started-with-ncbi-data-in-python-04-22/ -- description: A tutorial introducing the BioSamples database and the concept of a - biosample. It also provides website navigation tips, and directs users to more - information on accessing and downloading data from BioSamples. - name: BioSamples Quick tour - provider: EMBL-EBI - topics: - - Data Sharing - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/biosamples-quick-tour/ -- description: What metadata is and why it is important to keep track of this information - in biological experiments. - name: Describing data consistently - provider: EMBL-EBI - topics: - - Data Planning - - 'Data Sharing ' - type: Short Video - url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/what-makes-a-good-bioinformatics-database/describing-data-consistently/ -- description: Basic tips on managing and sharing data to maximise its re-use in the - future. - name: Tips on managing and sharing data - provider: EMBL-EBI - topics: - - Data Planning - type: Guide - url: https://www.ebi.ac.uk/training/online/courses/bioinformatics-terrified/tips-on-managing-and-sharing-data/ -- description: These slides focus on topics such as discipline-specific repositories, - generalist repositories, the FAIRDOM platform, and reproducible models in FAIRDOM. - name: Data publishing and archival - provider: ELIXIR Luxembourg - topics: - - Genomics - - Data Planning - type: Slides - url: https://zenodo.org/record/5524794 -- description: ' - - A workshop covering how to use AWS services like Athena to mine metadata from - the NCBI SRA database for dataset selection, perform sequence alignment analysis - with MagicBlast, and visualize aligned data in the NCBI Genome Data Viewer browser - application.' - name: An Introduction to NCBI Cloud Computing for Biologists - provider: NCBI - topics: - - Genomics - - Data Collection - - Data Analysis - - Data Reuse - type: Workshop - url: https://www.nlm.nih.gov/oet/ed/ncbi/2022_07_cloud.html -- description: A tutorial covering the importance of data submission, metadata templates - like MIAME and MINSEQE, submission timelines, and submission locations for functional - genomics data (e.g. ArrayExpress and GEO). It also discusses secondary databases - like Expression Atlas. - name: Functional Genomics - Submitting data - provider: EMBL-EBI - topics: - - Genomics - - Data Sharing - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/functional-genomics-iii-submitting-data/ -- description: A webinar offering an overview of EGA, discussing its controlled access - data, the process for gaining access through the Data Access Committee, the use - of DUO ontology for tagging data, and a live demo of pyEGA3 for downloading permitted - data. - name: Introduction to exploring genome-phenome data with EGA - provider: EMBL-EBI - topics: - - Genomics - - Data Reuse - type: Webinar - url: https://www.ebi.ac.uk/training/events/introduction-exploring-genome-phenome-data-ega/ -- description: A webinar offering a detailed guide on submitting data to the GWAS - Catalog, including user account setup, data format conversion, metadata provision, - and validation using a command-line tool, with an emphasis on explaining metadata - columns. - name: Submitting your genome wide association study data to the GWAS Catalog - provider: EMBL-EBI - topics: - - Genomics - - Data Sharing - type: Webinar - url: https://www.ebi.ac.uk/training/events/submitting-your-genome-wide-association-study-data-gwas-catalog/ -- description: A webinar introducing the background of the European Nucleotide Archive - (ENA), data and metadata models, submission and retrieval processes, submission - methods, and tools for data download. - name: Nucleotide sequencing data submission and retrieval at the ENA - provider: EMBL-EBI - topics: - - Genomics - - Data Collection - - Data Sharing - - Data Reuse - type: Webinar - url: https://www.ebi.ac.uk/training/events/nucleotide-sequencing-data-submission-and-retrieval-ena/ -- description: A webinar providing an overview of the European Variation Archive (EVA) - and its integration with other EBI resources, a live demo of the EVA interface - for accessing data via web, FTP, or API, and clarification on using SS and RS - IDs for variant access/reference. - name: Variant submission and data access at the European Variation Archive - provider: EMBL-EBI - topics: - - Data Sharing - - Data Reuse - type: Webinar - url: https://www.ebi.ac.uk/training/events/variant-submission-and-data-access-european-variation-archive/ -- description: 'A tutorial introducing ArrayExpress and describing Annotare tool and - MAGE-TAB spreadsheet method for data submission. ' - name: ArrayExpress in BioStudies - provider: EMBL-EBI - topics: - - Data Sharing - type: Online tutorial - url: https://www.ebi.ac.uk/training/online/courses/arrayexpress-in-biostudies/#vf-tabs__section--overview diff --git a/_data/sidebars/main.yml b/_data/sidebars/main.yml index 344bfd8..521bab2 100644 --- a/_data/sidebars/main.yml +++ b/_data/sidebars/main.yml @@ -7,6 +7,8 @@ subitems: subitems: - title: Data management url: /data_management + - title: Structural biology + url: /structural_biology - title: About url: /about - title: Contact us diff --git a/_data/topnav.yml b/_data/topnav.yml index 8b7b132..16118b7 100644 --- a/_data/topnav.yml +++ b/_data/topnav.yml @@ -1,6 +1,2 @@ -## -## if you want to list an external url, use external_url instead of url. the theme will apply a different link base. -#subitems: -#- title: About -# url: /index - \ No newline at end of file +## The learning library does not use topnav.yml. Use /sidebars/main.yml to adjust the navigation buttons +## See https://github.com/AustralianBioCommons/how-to-guide-template/blob/main/_data/topnav.yml and https://australianbiocommons.github.io/how-to-guide-template/ for an example of how the topnav works diff --git a/_includes/resource-table-all.html b/_includes/resource-table-all.html index a4727e4..591ce5a 100644 --- a/_includes/resource-table-all.html +++ b/_includes/resource-table-all.html @@ -1,48 +1,46 @@ {%- if include.tag %} -{%- assign tools = site.data.tool_and_resource_list | add_related_pages | where:"related_pages", include.tag | sort_natural: "name" %} +{%- assign resources = site.data.all_content_list | add_collection | where:"collection", include.tag | sort_natural: "name" %} {%- else %} -{%- assign tools = site.data.tool_and_resource_list | add_related_pages | sort_natural: "name" %} +{%- assign resources = site.data.all_content_list | add_collection | sort_natural: "name" %} {%- endif %} -{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %} -{%- unless tools.size == 0 or tools == nil %} -Skip tool table +{%- unless resources.size == 0 or resources == nil %} +Skip resource table
- +
- - {%- for tool in tools %} + {%- for resource in resources %} - {% if tool.url %} - + {% if resource.url %} + {%- else %} - + {%- endif %} - - - - + + + {%- endfor %}
Resource Description Topic(s) FormatProvider
{{tool.name}}{{resource.name}}{{tool.name}}{{resource.name}}{{tool.description}} - {%- if tool.instance_of or tool.how_to_access or instances_tool != 0 and total_county_tools != 0 and include.tag != nil %} - {%- assign linked_tool = site.data.tool_and_resource_list | where:"id", tool.instance_of | first %} + {{resource.description}} + {%- if resource.instance_of or resource.how_to_access or instances_resource != 0 and total_county_resources != 0 and include.tag != nil %} + {%- assign linked_resource = site.data.all_content_list | where:"id", resource.instance_of | first %}
- {%- if tool.how_to_access %} - + {%- if resource.how_to_access %} + {%- endif %}
{%- endif %} 		{{tool.Topics}}{{tool.type}}{{tool.provider}}{{resource.topics}}{{resource.type}}{{resource.provider}}
{%- endunless %} -
+
diff --git a/pages/structural_biology.md b/pages/structural_biology.md new file mode 100644 index 0000000..443724d --- /dev/null +++ b/pages/structural_biology.md @@ -0,0 +1,12 @@ +--- +title: Structural biology +type: Collection +page_id: structural_biology +contributors: +description: +affiliations: +datatable: true +--- +The structural biology collection is maintained by the Australian Structural Biology Community and endorsed by Australian BioCommons. + +### Browse the collection diff --git a/scripts/table_conversion.py b/scripts/table_conversion.py index 8f82c81..74cb2a0 100644 --- a/scripts/table_conversion.py +++ b/scripts/table_conversion.py @@ -7,24 +7,24 @@ import yaml import os -# --------- Variables - set to match your google sheet as needed --------- +# --------- Variables - set to match the desired import google sheet as needed --------- google_id = "1uIBItELephFZNjC4UPoegQpo1pIzY15IjOgX8q33slU" gid = "0" url = f"https://docs.google.com/spreadsheets/d/{google_id}/export?format=csv&gid={gid}" -output_path = "_data/tool_and_resource_list.yml" +output_path = "_data/all_content_list.yml" rootdir = '../pages' allowed_providers = ['provider'] # --------- Converting the table --------- - -print(f"----> Converting google table to {output_path} started.") -resource_table = pd.read_csv(url, dtype={'name': str, 'url': str, 'description': str, 'related_pages': str, 'Topics': str, 'type': str, 'provider': str}) # --------- Each column header in the google sheet needs to be included in the dtype= code and defined as a string (str) --------- +print(f"----> Converting google table to {output_path} started.") +resource_table = pd.read_csv(url, dtype={'name': str, 'url': str, 'description': str, 'collection': str, 'topics': str, 'type': str, 'provider': str}) +# --------- The collection column sets which collection the row item will be included in for the Learning Library site. The topics column allows multiple entries, must be separated by a comma and a space --------- resource_list = resource_table.to_dict("records") clean_resource_list = [] for resource in resource_list: - if not pd.isna(resource['related_pages']): - category_list = resource['related_pages'].rsplit(sep=", ") + if not pd.isna(resource['collection']): + category_list = resource['collection'].rsplit(sep=", ") else: category_list = "" # registry_dict = {} @@ -36,7 +36,7 @@ clean_resource_list.append(clean_resource) # clean_resource['registry'] = registry_dict if category_list != "": - clean_resource['related_pages'] = category_list + clean_resource['collection'] = category_list print(os.getcwd()) with open(output_path, 'w+') as yaml_file: