seek4science · PhilReedData · Jun 4, 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
@@ -1,6 +1,6 @@
 #baseurl: /seek
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@4.1.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@4.2.0
 
 current_seek_version: "1.16.2"
 current_docker_tag: "1.16"
@@ -9,8 +9,13 @@ plugins:
   - jekyll-sitemap
   - jekyll-redirect-from
 
+# Do not remove the site.title. It's part of the ETT configuration.
 title: "FAIRDOM-SEEK Documentation"
 
+seek_instance:
+  name: "FAIRDOM-SEEK"
+  url: "https://fairdomhub.org"
+
 exclude:
  - Gemfile*
  - .gitignore
@@ -35,10 +40,10 @@ defaults:
     values:
       sidebar: technical_guide
 
-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/_data/sidebars/user_guide.yml b/_data/sidebars/user_guide.yml
@@ -8,13 +8,13 @@ subitems:
     - title: Browsing content
       url: /help/user-guide/browsing
   - title: Profile
-    description: Registering and logging into FAIRDOM-SEEK, managing your account and identities, editing your profile.
+    description: Registering and logging in, managing your account and identities, editing your profile.
     subitems:
     - title: Registration and Login
       subitems:
-      - title: Registering in FAIRDOM-SEEK
+      - title: User registration
         url: /help/user-guide/registering
-      - title: Logging into FAIRDOM-SEEK via LS Login
+      - title: Logging in via LS Login
         url: /help/user-guide/aai
       - title: Managing your identities/alternative login methods
         url: /help/user-guide/managing-identities
@@ -68,7 +68,7 @@ subitems:
     subitems:
     - title: Introduction to the ISA structure
       subitems:
-      - title: Visualising ISA structure in FAIRDOM-SEEK
+      - title: Visualising the ISA structure
         url: /help/user-guide/isa-overview
       - title: Generating the ISA structure
         url: /help/user-guide/generating-the-isa-structure
@@ -98,7 +98,7 @@ subitems:
   -
     #hr: true
     title: Assets
-    description: Adding different types of assets to FAIRDOM-SEEK, creating new asset versions.
+    description: Adding different types of assets, creating new asset versions.
     subitems:
     - title: Adding assets (data, models, SOPs, publications)
       url: /help/user-guide/adding-assets
@@ -175,16 +175,16 @@ subitems:
   -
     #hr: true
     title: Integrations
-    description: Using FAIRDOM-SEEK and openBIS or Copasi, compliance with ISA-JSON schemas.
+    description: Integration with openBIS or Copasi, compliance with ISA-JSON schemas.
     subitems:
-    - title: Using FAIRDOM-SEEK with openBIS
+    - title: openBIS connections
       url: /help/user-guide/openbis
-    - title: Using Copasi with FAIRDOM-SEEK
+    - title: Using Copasi
       url: /help/user-guide/copasi-button
   -
     #hr: true
     title: User guide for API
-    description: Introduction to the FAIRDOM-SEEK API.
+    description: Introduction to the API.
     subitems:
     - title: API Introduction
       url: /help/user-guide/api
@@ -196,13 +196,13 @@ subitems:
         url: /help/archived
       - title: Data and model annotation
         subitems:
-         - title: Minimum metadata guidelines for FAIRDOM-SEEK
+         - title: Minimum metadata guidelines
            url: /help/metadata-guidelines
          - title: A Quick guide to using the ISA structure
            url: /help/isa-guide
          - title: ISA best practice
            url: /help/isa-best-practice
-         - title: "Transcriptomics: guidelines for FAIRDOM-SEEK templates"
+         - title: "Transcriptomics: guidelines for metadata templates"
            url: /help/transcriptomics-guidelines
          - title: Proteomics guidelines
            url: /help/proteomics-guidelines

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 +1,5 @@
 ---
-title: Minimum metadata guidelines for FAIRDOM-SEEK
+title: Minimum metadata guidelines
 redirect_from: "/metadata-guidelines.html"
 ---
 
@@ -8,8 +8,6 @@ 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 +1,12 @@
 ---
-title: "Transcriptomics: Guidelines for FAIRDOM-SEEK templates"
+title: "Transcriptomics: Guidelines for metadata templates"
 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/aai.md b/help/user-guide/aai.md
@@ -4,12 +4,12 @@ title: Logging into via LS Login
 
 
 {% include callout.html type="note" content="This section assumes you have an LS Login account (or your organization is connected to LS Login),
-and LS Login authentication is enabled on the SEEK instance you are using. For more information on LS Login, please
+and LS Login authentication is enabled on the FAIRDOM-SEEK instance you are using. For more information on LS Login, please
 see their [documentation](https://lifescience-ri.eu/ls-login/documentation/user-documentation/user-documentation.html){:target=\"_blank\"}." %}
 
 Already got a SEEK account? See how to [add LS Login to your account]({{ "/managing-identities#add-identity" | relative_url }}) instead.
 
-If enabled on the SEEK instance you are using, you will see a tab on the login form titled "LS Login"
+If enabled on the FAIRDOM-SEEK instance you are using, you will see a tab on the login form titled "LS Login"
 
 Clicking this will switch to the LS Login tab and present the LS Login login button.
 
@@ -29,7 +29,7 @@ Note: this will likely look different to the screenshot below.
 ![Institution login form]({{ "/images/user-guide/omniauth/inst_login.png" | relative_url }}){:.screenshot}
 
 After logging in through your institution, you may then be presented with a personal information consent page,
-which outlines what personal data will be provided by LS Login to the SEEK instance.
+which outlines what personal data will be provided by LS Login to the FAIRDOM-SEEK instance.
 
 At a minimum, the identifier must be provided, or login is not possible. Any other information is used solely to
 populate fields in your SEEK profile.

diff --git a/help/user-guide/adding-assets.md b/help/user-guide/adding-assets.md
@@ -1,8 +1,8 @@
 ---
-title: Adding assets (Data, Models, SOPs, Presentations, Documents) to FAIRDOM-SEEK
+title: Adding assets (Data, Models, SOPs, Presentations, Documents)
 ---
 
-To add a data file to SEEK, select Create from the menu bar, and select the appropriate asset from the drop down menu.
+To add a data file to {{ site.seek_instance.name | default: "FAIRDOM-SEEK" }}, select Create from the menu bar, and select the appropriate asset from the drop down menu.
 
 ![add data 1]({{ "/images/user-guide/add_data_1.png" | relative_url }}){:.screenshot}
 

diff --git a/help/user-guide/aliases.md b/help/user-guide/aliases.md
@@ -4,14 +4,13 @@ title: Aliases across FAIRDOM-SEEK instances
 
 FAIRDOM-SEEK instances are highly customisable. Functionality such as e.g. the ISA structure, ISA-JSON compliant experiments and the different asset types need to be enabled by an instance admin. Therefore, some functionality described in this general user guide might not be available on your local instance.
 
-The names of different features and functions may vary across FAIRDOM-SEEK instances. This general user guide includes the default or most common names. Below is a look-up list for the most common names that are included in the user guide, and what they may be called in a different instance. Note, this list is not complete. 
+The names of different features and functions may vary across FAIRDOM-SEEK instances. This general user guide includes the default or most common names. Below is a look-up list for the most common names that are included in the user guide, and what they may be called in a different instance. Note, this list is not complete.
 
 ## Look up aliases
 
- Name in user guide | Alias | Where the alias is used 
---------------------|-------|-------------------------
-Project | Team | WorkflowHub
-Programme | Space | WorkflowHub
-SOP | Protocol | DataHub
-
-
+ | Name in user guide | Alias                      | Where the alias is used |
+ | ------------------ | -------------------------- | ----------------------- |
+ | Project            | Team                       | WorkflowHub             |
+ | Programme          | Space                      | WorkflowHub             |
+ | SOP                | Protocol                   | DataHub                 |
+ | Template           | Experiment Sample Template | DataHub                 |
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
@@ -25,7 +25,7 @@ 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 +1,5 @@
 ---
-title: Browsing content on FAIRDOM-SEEK
+title: Browsing content
 ---
 
 

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 +1,5 @@
 ---
-title: Using Copasi in FAIRDOM-SEEK
+title: Using Copasi
 ---
 
 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.