seek4science · kdp-cloud · Apr 24, 2025 · Apr 24, 2025 · Apr 24, 2025 · Apr 24, 2025
diff --git a/.gitignore b/.gitignore
@@ -1,27 +1,11 @@
 syntax: glob
 .idea/
 _site/
-
 *.DS_Store
 *~
-
 *.~lock*
-
 *.orig
-
 Gemfile.lock
-
 .ruby-version
-
-#seek application folders that may hang around
-filestore*/
-config/
-coverage/
-log/
-public/
-solr/
-tmp/
 .bundle/
-db/
-filestore
-vendor/
+.vscode/
diff --git a/_config.yml b/_config.yml
@@ -9,7 +9,9 @@ plugins:
   - jekyll-sitemap
   - jekyll-redirect-from
 
-title: "FAIRDOM-SEEK Documentation"
+seek_instance:
+  name: "FAIRDOM-SEEK"
+  url: "https://fairdomhub.org"
 
 exclude:
  - Gemfile*
@@ -35,10 +37,10 @@ defaults:
     values:
       sidebar: technical_references
 
-theme_variables: 
+theme_variables:
   #git_host: GitHub
   #back_to_top: true
-  #github_buttons: 
+  #github_buttons:
   #  position: top
   #  edit_me: true
   #  open_issue: true

diff --git a/_layouts/instance-specific.html b/_layouts/instance-specific.html
@@ -0,0 +1,15 @@
+---
+layout: page
+---
+
+{{ content }}
+
+<script type="text/javascript">
+    let introElement = document.getElementById("intro");
+    if (introElement) {
+        let pageTitle = introElement.querySelector("h1");
+        if (pageTitle) {
+            pageTitle.innerHTML = pageTitle.innerHTML.replace(/FAIRDOM-SEEK/g, "{{ site.seek_instance.name }}");
+        }
+    }
+</script>
diff --git a/help/archived.md b/help/archived.md
@@ -2,7 +2,7 @@
 title: Archived help and guidelines
 ---
 
-The FAIRDOM-SEEK help and guidelines are written for users of any FAIRDOM-SEEK instance.
+The {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} help and guidelines are written for users of any FAIRDOM-SEEK instance.
 
 {% assign guide_url = site.baseurl | append: '/help/user-guide' %}
 {% assign callout_content = "Please see the [user guide](" | append: guide_url | append: ") for the latest help." %}

diff --git a/help/metadata-guidelines.md b/help/metadata-guidelines.md
@@ -1,5 +1,6 @@
 ---
 title: Minimum metadata guidelines for FAIRDOM-SEEK
+layout: instance-specific
 redirect_from: "/metadata-guidelines.html"
 ---
 
@@ -8,8 +9,6 @@ redirect_from: "/metadata-guidelines.html"
 {% assign callout_content = "This guide has been archived. Please see the [user guide](" | append: guide_url | append: ") for the latest help." %}
 {% include callout.html type="warning" content=callout_content %}
 
-{% include callout.html type="note" content="This guide refers to SEEK, but is also relevant for [FAIRDOMHUB](https://www.fairdomhub.org/), which is an instance of SEEK." %}
-
 The more metadata you provide for your assets in the SEEK, the easier it is to find them and to compare them with other assets. If you provide assets with very little metadata, these will also be displayed (in accordance with access control policies set by you), but they may be hard to interpret for other people.
 
 In addition to SEEK data sharing guidelines, some types of data have minimum metadata requirements for publication, for example, microarray data must be MIAME compliant. Following the guidelines for SEEK metadata should ensure that when you come to publish, you have already met these requirements.

diff --git a/help/transcriptomics-guidelines.md b/help/transcriptomics-guidelines.md
@@ -1,14 +1,13 @@
 ---
 title: "Transcriptomics: Guidelines for FAIRDOM-SEEK templates"
+layout: instance-specific
 redirect_from: "/transcriptomics-guidelines.html"
 ---
 
 {% assign guide_url = site.baseurl | append: '/help/user-guide' %}
 {% assign callout_content = "This guide has been archived. Please see the [user guide](" | append: guide_url | append: ") for the latest help." %}
 {% include callout.html type="warning" content=callout_content %}
 
-{% include callout.html type="note" content="This guide refers to SEEK, but is also relevant for [FAIRDOMHUB](https://www.fairdomhub.org/), which is an instance of SEEK." %}
-
 The MIAME standard and the associated MAGE-ML format are well established in the transcriptomics community and adherence to MAGE-ML is becoming increasingly important for publishing data.
 
 MAGE-TAB is a tab delimited representation of MAGE-ML. It allows users to construct MIAME compliant excel spreadsheets. The ISA-TAB specification also allows an export to MAGE-TAB format.

diff --git a/help/user-guide/adding-assets.md b/help/user-guide/adding-assets.md
@@ -1,5 +1,6 @@
 ---
 title: Adding assets (Data, Models, SOPs, Presentations, Documents) to FAIRDOM-SEEK
+layout: instance-specific
 ---
 
 To add a data file to SEEK, select Create from the menu bar, and select the appropriate asset from the drop down menu.

diff --git a/help/user-guide/api.md b/help/user-guide/api.md
@@ -2,20 +2,20 @@
 title: API Introduction
 ---
 
-FAIRDOM-SEEK includes a [JSON](https://www.json.org/) Application
+{{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} includes a [JSON](https://www.json.org/) Application
 Programming Interface (API) that allows the **searching,
-listing, reading, updating and creating** of many items in SEEK, 
+listing, reading, updating and creating** of many items in SEEK,
 along with their attributes.
 
 The API conforms to the [JSON API](http://jsonapi.org) specification which
 describes a standard way of representing APIs in JSON.
 
 Technical details about the JSON structures and available endpoints
- comes bundled with FAIRDOM-SEEK and can be found served from:
+ comes bundled with {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} and can be found served from:
 
     http://<host>:<port>/api
 
-For example, on the FAIRDOMHub it is [https://fairdomhub.org/api](https://fairdomhub.org/api), 
+For example, on the FAIRDOMHub it is [{{ site.seek_instance.url | default: "https://fairdomhub.org" }}/api]({{ site.seek_instance.url | default: "https://fairdomhub.org" }}/api),
 or for a local running instance it would be [http://localhost:3000/api](http://localhost:3000/api)
 
 There are also some examples that are available as Jupyter notebook scripts. They were created for training events, and give
@@ -26,7 +26,7 @@ a general overview and walk through some typical scenarios. They can be found at
 
 The API supports [Basic Authentication](https://en.wikipedia.org/wiki/Basic_access_authentication), OAuth and API Tokens.
 
-More details can be found in [FAIRDOMHub API Docs](https://fairdomhub.org/api#section/Authentication)
+More details can be found in [{{ site.seek_instance.name }} API Docs]({{ site.seek_instance.url | default: "https://fairdomhub.org" }}/api#section/Authentication)
 
 The API can also be used without any authentication,
 in which case only publicly viewable information will

diff --git a/help/user-guide/browsing.md b/help/user-guide/browsing.md
@@ -1,5 +1,6 @@
 ---
 title: Browsing content on FAIRDOM-SEEK
+layout: instance-specific
 ---
 
 

diff --git a/help/user-guide/bulk-change-sharing-permission.md b/help/user-guide/bulk-change-sharing-permission.md
@@ -19,7 +19,7 @@ you can see all the items you own in two lists:
 
 Note that:
 * The item list excludes **Project**, **Institution** and **Publication** since these are always publicly visible;
-* The items are not visually grouped by project, but they are visualized in descending order based on FAIRDOM-SEEK ID;
+* The items are not visually grouped by project, but they are visualized in descending order based on {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} ID;
 * You can view current permissions of each item by clicking the item's name;
 * Select items you want to change their sharing permissions by checking the checkbox;
 * If no items are selected before clicking the “next” button, the error message “Please choose at least one item!” will pop up.

diff --git a/help/user-guide/copasi-button.md b/help/user-guide/copasi-button.md
@@ -1,5 +1,6 @@
 ---
 title: Using Copasi in FAIRDOM-SEEK
+layout: instance-specific
 ---
 
 You can download a public SBML format **model** to a locally installed Copasi application and start the simulation in Copasi.

diff --git a/help/user-guide/create-a-project.md b/help/user-guide/create-a-project.md
@@ -14,7 +14,7 @@ A member of the Project will also be related to an Institution for the context o
 
 ## What is a Programme
 
-If configured to be enabled, FAIRDOM-SEEK may also have Programmes. Programmes are an umbrella that contains one or more Projects. They are a self-administered area, that describes a broad activity (usually related to a funded grant), such as a consortium, or a long-running activity that will need additional Projects.
+If configured to be enabled, {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} may also have Programmes. Programmes are an umbrella that contains one or more Projects. They are a self-administered area, that describes a broad activity (usually related to a funded grant), such as a consortium, or a long-running activity that will need additional Projects.
 
 Once approved, The Programme will have a [Programme Administrator](roles#programme-administrator) who is free to immediately create additional Projects without requiring additional approval.
 
@@ -24,7 +24,7 @@ For users that just require a single Project, and don't require a Programme, a s
 
 ## Creating a Project
 
-You will first be prompted to create (or [Join a Project](join-a-project)) following registering a new FAIRDOM-SEEK account. If you are already a member and wish to add additional Projects, you can choose to create a Project from the _Create_ menu in the top bar.
+You will first be prompted to create (or [Join a Project](join-a-project)) following registering a new {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} account. If you are already a member and wish to add additional Projects, you can choose to create a Project from the _Create_ menu in the top bar.
 
 ### Choosing a Programme
 
@@ -55,5 +55,5 @@ If describing a new Institution only the title is required, but you can also pro
 
 If you are creating a Project within a Programme you administer, then there is no approval step. You will be shown a page to review the details and then create straight away.
 
-Otherwise, an appropriate administrator will be notified by email about your request. They will also be notified directly when using FAIRDOM-SEEK. The administrator will be shown a page that allows them to quickly review the details and either accept or reject the request, and in either case you will be notified by email.
+Otherwise, an appropriate administrator will be notified by email about your request. They will also be notified directly when using {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}. The administrator will be shown a page that allows them to quickly review the details and either accept or reject the request, and in either case you will be notified by email.
 
diff --git a/help/user-guide/definitions.md b/help/user-guide/definitions.md
@@ -1,9 +1,10 @@
 ---
 title: FAIRDOM-SEEK Definitions
 redirect_from: /definitions
+layout: instance-specific
 ---
 
-Definition of terms used in FAIRDOM-SEEK.
+Definition of terms used in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}.
 
 ---
 
@@ -79,7 +80,7 @@ Alias for Project.
 ## Experiments
 Scientific procedures undertaken to make a discovery, test a hypothesis or demonstrate a fact.
 ### Assay
-<!--From user guide:-->An assay is in general an experiment that converts either a material or data sample, into a new material or data sample, via a protocol. 
+<!--From user guide:-->An assay is in general an experiment that converts either a material or data sample, into a new material or data sample, via a protocol.
 
 <!--From info icon:-->An Assay is in general the application of a process (SOP) that converts an input material or data (incoming samples) into a new material or data (outgoing samples). An Assay must belong to one Study.
 ### Assay design
@@ -113,7 +114,7 @@ The ISA (Investigation, Study, Assay) is a general purpose framework for describ
 * Graph: It displays as a graph, showing the overall ISA structure. It shows a graphical view of highlighting the item within the network.
   * all nodes: Toogle between expanding all nodes in the graph, or showing just the nearest neighbours.
   * Reset: It resets the graph to its original state, reverting any changes to zoom or moved nodes.
-* Split: The Split view provides a combination of the Tree and Graph view, with the tree shown on the right. 
+* Split: The Split view provides a combination of the Tree and Graph view, with the tree shown on the right.
 * Tree: It displays with a folder like tree view. The tree view is the default view, and shows the ISA structure as folders, similar to a file browser.
 
 
@@ -289,7 +290,7 @@ To visualise samples from one Sample Type in a searchable table.
 
 ## Actions
 * Administer Project members
-  * Add members: to add registered users to the project, using one or more institutions. 
+  * Add members: to add registered users to the project, using one or more institutions.
   * Mark/Unmark user as inactive: to manage items of registered users that are not using the platform anymore.
   * Pending changes: list of changes that have not been confirm yet. Pending changes will not be applied if not confirmed.
   * Project members: list of all members of the project, grouped by institution. A project member can be listed multiple times if he/she has been added to the project using multiple institutions.
@@ -351,14 +352,13 @@ Tab showing items related to the selected one.
 ### Search
 To search for a specific query. The search will attempt to find partial matches for the search term in all item categories. The search can be restricted to one specific item category (e.g. Documents), as for browsing.
 #### External
-The search can be extended to incude results from external online resources Linked? Integrated? with FAIRDOM-SEEK.
-#### Advanced search with filtering
-To access the query and the faceted navigation option for one specific item category (e.g. Documents). 
+The search can be extended to include results from external online resources Linked? Integrated? with {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}.
+To access the query and the faceted navigation option for one specific item category (e.g. Documents).
 
 ### Storage Usage
-Storage metrics, for Programmes and Projects, available to FAIRDOM-SEEK administrator. It provides the total size of all Programme or Project assets.
+Storage metrics, for Programmes and Projects, available to {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} administrator. It provides the total size of all Programme or Project assets.
 ### Change picture or avatar
-Custom graphic for a secific item.
+Custom graphic for a specific item.
 ### (number)
 Number of items of a category (e.g. Documents) visible to you.
 ### (number + number)
@@ -371,7 +371,7 @@ Number of items of a category (e.g. Documents) visible to you.
 ### Bio.tools
 To fetch bio.tools identifiers.
 ### Copasi
-To download a public SBML format model from FAIRDOM-SEEK to a locally installed Copasi application and start the simulation in Copasi.
+To download a public SBML format model from {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} to a locally installed Copasi application and start the simulation in Copasi.
 ### JWS online
 To visualise the model in JWS online.
 ### DOI minting
@@ -381,9 +381,9 @@ To apply LifeMonitor algorithm to workflows.
 ### NeLS
 To enable linking of datasets stored in the Norwegian e-infrastructure for Life Sciences (NeLS), as well as upload and access of datasets to/from NeLS through SEEK
 ### OpenBIS
-To fetch and register OpnBIS elements in FAIRDOM-SEEK.
+To fetch and register OpenBIS elements in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}.
 ### Publish in Zenodo
-To publish a snapshot to Zenodo from FAIRDOM-SEEK.
+To publish a snapshot to Zenodo from {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}.
 <!--### Project folders
 Free folders within a project to group registered items.-->
 ### Single page

diff --git a/help/user-guide/general-attributes.md b/help/user-guide/general-attributes.md
@@ -1,6 +1,7 @@
 ---
 title: Generic linking variables in FAIRDOM-SEEK
 redirect_from: "/help/user-guide/generic-linking-variables.html"
+layout: instance-specific
 ---
 
 

diff --git a/help/user-guide/index.md b/help/user-guide/index.md
@@ -2,9 +2,10 @@
 title: FAIRDOM-SEEK User Guide
 redirect_from:
   - /help
+layout: instance-specific
 ---
 
-The FAIRDOM-SEEK user guide is written for users of any FAIRDOM-SEEK instance. The pages are organised by sections on the left. You can also search at the top-right of any page.
+The {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }} user guide is written for users of any FAIRDOM-SEEK instance. The pages are organised by sections on the left. You can also search at the top-right of any page.
 
 <i class="fa-solid fa-user-group fa-5x"></i> <i class="fa-solid fa-book fa-5x"></i>
 

diff --git a/help/user-guide/join-a-project.md b/help/user-guide/join-a-project.md
@@ -44,5 +44,5 @@ You also have the option to provide a comment to describe why you wish to join t
 
 ### Approval step
 
-Your request will be sent to the Project administrators, both through email or a notification in FAIRDOM-SEEK. You will either then be approved and added to the Project, or your request may be rejected. Either way, you will be notified by email of the outcome.
+Your request will be sent to the Project administrators, both through email or a notification in {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}. You will either then be approved and added to the Project, or your request may be rejected. Either way, you will be notified by email of the outcome.
 
diff --git a/help/user-guide/openbis.md b/help/user-guide/openbis.md
@@ -1,5 +1,6 @@
 ---
 title: Using FAIRDOM-SEEK with openBIS
+layout: instance-specific
 ---
 
 ## Enabling openBIS in SEEK

diff --git a/help/user-guide/registering.md b/help/user-guide/registering.md
@@ -1,5 +1,6 @@
 ---
 title: Registering in FAIRDOM-SEEK
+layout: instance-specific
 ---
 
 In order to register yourself in SEEK, you need to click the Register button in the top right hand corner of SEEK.

diff --git a/help/user-guide/templates/master-v1.md b/help/user-guide/templates/master-v1.md
@@ -46,7 +46,7 @@ _**10.**_ If you wish to link the Assay to an existing SOP, this should contain
 ### * SEEK ID's
 
 The SEEK ID should be the full resolvable _persistent identifier_, including the host. This can be found for any item in SEEK, and generally matches
-the URL. This isn't always the case though, such as if a SEEK is running with different aliases. For example https://fairdomhub.org/projects/19.
+the URL. This isn't always the case though, such as if a SEEK is running with different aliases. For example {{ site.seek_instance.url | default: "https://fairdomhub.org" }}/projects/19.
 
 It can be found near the top of page, under the description.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -44,5 +44,5 @@ You also have the option to provide a comment to describe why you wish to join t

		### Approval step

		Your request will be sent to the Project administrators, both through email or a notification in FAIRDOM-SEEK. You will either then be approved and added to the Project, or your request may be rejected. Either way, you will be notified by email of the outcome.
		Your request will be sent to the Project administrators, both through email or a notification in {{ site.seek_instance.name \| default: "FAIRDOM-SEEK" }}. You will either then be approved and added to the Project, or your request may be rejected. Either way, you will be notified by email of the outcome.