Add labid as tool_assembly

_data/CONTRIBUTORS.yaml

@@ -856,4 +856,7 @@ Rahuman Sheriff:
     orcid: 0000-0003-0705-9809
     affiliation: EMBL-EBI
     email: sheriff@ebi.ac.uk
-
+Laurent Thomas:
+    git: LauLauThom
+    orcid: 0000-0001-7686-3249
+    affiliation: EMBL Heidelberg

_data/affiliations.yaml

@@ -189,3 +189,9 @@
   expose: true
   type: institution
   url: https://ut.ee/
+- name: EMBL Heidelberg
+  type: institution
+  image_url: /images/institutions/EMBL_logo.svg
+  pid: https://ror.org/03mstc592
+  expose: yes
+  url: https://www.embl.org/

_data/news.yml

@@ -242,3 +242,7 @@
   date: 2026-03-02
   linked_pr: 1790
   description: A new "your domain" page about Agroecology was added. [Discover the page here](agroecology).
+- name: "New page: LabID tool assembly"
+  date: 2026-03-27
+  linked_pr: 1799
+  description: A new "tool assembly" page for LabID was added. [Discover the page here](labid_assembly).

_data/sidebars/data_management.yml

@@ -140,6 +140,8 @@ subitems:
         url: /galaxy_assembly
       - title: IFB
         url: /ifb_assembly
+      - title: LabID
+        url: /labid_assembly
       - title: Marine Metagenomics
         url: /marine_metagenomics_assembly
       - title: MOLGENIS

_data/tool_and_resource_list.yml

@@ -3558,3 +3558,9 @@
   id: proton-drive
   name: Proton Drive
   url: https://proton.me/drive
+- description: LabID is a data management solution for life-science institutes, featuring sample and dataset management, an inventory management system and an electronic lab notebook.
+  id: labid
+  name: LabID (Lab Integrated Data)
+  url: https://grp-gbcs.embl-community.io/labid-user-docs/
+  registry:
+    biotools: labid

pages/tool_assembly/labid_assembly.md

@@ -0,0 +1,74 @@
+---
+title: LabID
+contributors: [Laurent Thomas]
+editors: [Bert droesbeke, Federico Bianchini]
+page_id: labid
+page_img: labid.png
+affiliations: [EMBL Heidelberg]
+training:
+  - name: Tutorials from the LabID user-documentation
+    registry: LabID user-documentation
+    url: https://grp-gbcs.embl-community.io/labid-user-docs/training/
+related_pages: 
+  Your_tasks: [data_organisation, data provenance, storage, metadata, machine learning, single-cell sequencing]
+  Your_domain: [bioimaging_data, proteomics, plant sciences]
+description: LabID is an all-in-one FAIR data management platform for life sciences institutes. It allows keeping track of datasets, samples, workflows and inventory while featuring an Electronic Lab Notebook.
+---
+
+## What is LabID?
+{% tool "labid" %} is an open-source web-based platform for research data management in life science institutes, featuring sample and dataset management, an inventory management system and an electronic lab notebook. 
+
+LabID enables the recording of extensive experimental information about the provenance of data (samples, reagents, instruments, protocols, and assay parameters), and is designed to help individual scientists, research groups, and core facilities better manage, annotate, and share their research according to the FAIR principles. 
+
+LabID also features an electronic lab notebook, and a "workflow integration" to keep track of the execution of workflows such as {% tool "galaxy" %} or {% tool "nextflow" %}.  
+Workflows can be imported from various sources : {% tool "git" %} repositories ({% tool "github" %}, {% tool "gitlab" %}, {% tool "bitbucket" %}, etc.), {% tool "galaxy" %} instances, {% tool "workflowhub" %} or any platform that can provide workflows as Workflow {% tool "research-object-crate" %} (see [specification](https://w3id.org/workflowhub/workflow-ro-crate/)). Workflows can also be registered in LabID by simple drag-and-drop of local files.  
+Similarly, LabID supports importing and exporting workflow runs using the interoperable Workflow Run {% tool "research-object-crate" %} [specification](https://w3id.org/ro/wfrun/workflow/), which allows capturing both the data used and generated by the workflow, and metadata about the workflow execution (version of the workflow, parameter values, etc.). Such {% tool "research-object-crate" %} can be deposited to repositories such as {% tool "zenodo" %} or [RO-Hub](https://www.rohub.org/).  
+
+{% include image.html file="labid_overview.png" caption="Overview of LabID functionalities" alt="overview of LabID functionalities" %}
+
+## Key Features
+
+LabID is powered by a database that allows recording and interconnecting laboratory entities involved in life-science research (e.g. samples, reagents, instruments, and protocols). The result is a comprehensive knowledge graph capturing relationships between experimental components, enabling researchers to trace data provenance and share the full context of their research.
+
+- **Sample Management**: Track and organise biological samples with complete provenance information
+- **Dataset Management**: Register and annotate datasets with metadata and experimental parameters
+- **Electronic Lab Notebook**: Document experiments and observations
+- **Inventory System**: Manage reagents, instruments, and other lab resources
+- **Workflow Integration**: Keep track of workflow versions and workflow executions for platforms like {% tool "galaxy" %} or {% tool "nextflow" %}, and custom scripts. Import and export workflows from/to platforms like {% tool "workflowhub" %} and {% tool "git" %} repositories ({% tool "github" %}, {% tool "gitlab" %}, {% tool "bitbucket" %}, etc.).
+
+You can find a video with an overview of LabID's features [here](https://s3.embl.de/gbcs-public/labid-user-docs/labid-overview.mov). The video dates back to the time the software was called "Stocks". The features are the same, though, and the interface has only changed slightly since.  
+The LabID workflow integration is also summarised in the following [video](https://www.youtube.com/watch?v=2YH8TWH1Fg8).  
+
+## Which tasks can be solved with LabID?
+- referencing instruments, reagents and specimen available in an institute or research team
+- documenting assays performed in the lab, [associating](data_interlinking) them to the instrument, reagent and specimen used (e.g imaging of some tissue on a microscope)
+- [storing and archiving](data_organisation) of raw and processed data (e.g archiving a copy to a S3 bucket)
+- [adding metadata](metadata_management) to any entity using custom or controlled vocabulary  
+- [sharing](sharing) data, protocols, and assays with internal colleagues
+- document the execution of a script or workflow, together with the associated data and parameters. Export the resulting "workflow run" as a [Worklfow Run RO-Crate](https://www.researchobject.org/workflow-run-crate/profiles/workflow_run_crate/). 
+
+## How to access LabID?
+LabID is typically installed at the institute or research group level on a Unix server. The LabID user interface is accessible via a web browser, on a client machine that can access the server.    
+
+A public demo server is available at [https://labid-demo.embl.de/](https://labid-demo.embl.de/) so you can get a feeling of the user interface.  
+Most [trainings from the user-documentation](https://grp-gbcs.embl-community.io/labid-user-docs/training/) can also be followed along with this demo server.  
+
+## What technology is it built with?
+Under the hood, LabID is a client/server solution, similar in its architecture to e.g {% tool "omero" %}. It is made a several components :
+- the server or "backend", written in python and using the [Django framework](https://www.djangoproject.com/)
+- a postgres relational database, used to store reference to data and metadata 
+- the user interface or "frontend", written in [Vue.js](https://vuejs.org/)
+- a python library and command line interface, to automate e.g data-registration tasks
+
+
+## Links
+* [GitLab repositories](https://gitlab.com/lab-integrated-data)
+* [LabID user documentation](https://grp-gbcs.embl-community.io/labid-user-docs/)
+* [Slack channel](https://join.slack.com/t/labintegrateddata/shared_invite/zt-2eb4ivxyc-1C4RZP_For0uiWcHeiTw0Q)
+* [Demo server](https://labid-demo.embl.de/)
+
+## Funding
+LabID is developed and maintained by the [MODIS team](https://www.embl.org/groups/modis/) at the EMBL Heidelberg.
+
+The workflow integration of LabID was supported through the Open Science Clusters’ Action for Research and Society ([OSCARS](oscars-project.eu)) European project under grant agreement Nº101129751.  
+See [LabID PROV](https://oscars-project.eu/projects/labid-prov-tracking-and-sharing-data-provenance-ro-crate-lab-integrated-data). 

pages/your_tasks/data_organisation.md

@@ -1,11 +1,12 @@
 ---
 title: Data organisation
-contributors: [Siiri Fuchs, Minna Ahokas, Yvonne Kallberg, Ivan Mičetić, Marina Popleteeva, Naeem Muhammad]
+contributors: [Siiri Fuchs, Minna Ahokas, Yvonne Kallberg, Ivan Mičetić, Marina Popleteeva, Naeem Muhammad, Laurent Thomas]
 editors: [Bert Droesbeke, Flora D'Anna]
 description: Best practices to name and organise research data.
 page_id: data_organisation
 related_pages: 
-  Tool_assembly: [ome, transmed, xnat_pic]
+  Tool_assembly: [ome, transmed, xnat_pic, labid]
+  Your_tasks: [data_provenance]
 dsw:
 - name: How will you do file naming and file organization?
   uuid: 8e886b55-3287-48e7-b353-daf6ab40f7d8
@@ -150,3 +151,19 @@ The top folder should have a README.txt file describing the folder structure and
       README.txt            file and folder description  
 
 * Structured directories can be made by using {% tool "cookiecutter" %},a command-line utility that creates projects from cookiecutters (project templates), e.g. creating a Python package project from a Python package project template.
+
+## What software can I use for data organisation ?
+
+### Description
+While you can solely rely on conventions on filenaming and folder structures, some software also help dealing with the data and associated metadata. These software typically involve a database to record data entries, often providing support for associated metadata, and management of multiple users.    
+
+### Considerations
+The actual choice of software often depends on your application.  
+Those software are often meant to be installed on a server, such that they are available for a full institute or research team. 
+
+### Solutions
+Examples of such software include : 
+* {% tool "omero" %} suitable for microscopy and image-data management. It simplify organisation, browsing and visualisation of image datasets.    
+* {% tool "labid" %} for life-science in general, it features an electronic lab notebook, extensive functionalities for data and metadata management, curation and provenance visualisation.
+
+

pages/your_tasks/data_provenance.md

@@ -5,7 +5,7 @@ contributors: [Flora D'Anna, Korbinian Bösl, Nazeefa Fatima]
 editors: [Bert Droesbeke, Flora D'Anna, Korbinian Bösl]
 page_id: data_provenance
 related_pages: 
-  Tool_assembly: []
+  Tool_assembly: [ome, labid]
 training:
   - name:
     registry:
@@ -46,6 +46,6 @@ However, knowing what’s the best way to document provenance can be challenging
 - Implement serialisation specification of the [PROV-MODEL](https://www.w3.org/TR/prov-overview/) in your data management tools to record provenance in machine-actionable format (RDF, Linked data, owl, xml, etc.).
 - Use [RO-Crate specifications](https://www.researchobject.org/ro-crate/1.1/provenance.html) and/or specific profiles for provenance (e.g., [RO-Crate profiles to capture the provenance of workflow runs](https://www.researchobject.org/workflow-run-crate/)).
 - Make use of tools and software that help you record provenance in a manual or an automated way. Use:
-  - Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS) or similar tools.
+  - Electronic Data Capture (EDC) systems, Laboratory Information Management Systems (LIMS) or similar tools (such as {% tool "labid" %}).
   - Workflow management systems (such as Kepler, {% tool "galaxy" %}, Taverna, VisTrails); provenance information embedded in such software or tools are usually available to users of the same tool or can be exported as separated file in several formats, such as {% tool "research-object-crate" %}.
   - Registries such as {% tool "workflowhub" %}.

pages/your_tasks/metadata_management.md

@@ -5,7 +5,7 @@ editors: [Flora D'Anna, Marina Popleteeva, Nazeefa Fatima, Niclas Jareborg]
 description: How to document and describe your data.
 page_id: metadata
 related_pages:
-  Tool_assembly: [nels, transmed, plant_geno_assembly, marine_assembly]
+  Tool_assembly: [nels, transmed, plant_geno_assembly, marine_assembly, labid]
 dsw:
 - name: Will the metadata be available even when the data no longer exists?
   uuid: 3b3fbcc6-c405-4151-8dce-e11dbd46b1bd
@@ -54,7 +54,7 @@ Due to the large variety of experiments, techniques and collaborative studies th
 * There are many appropriate tools for data documentation during the project. Check with your institute to know what is offered.
   * Electronic Lab Notebooks (ELNs) are usually better for more disparate and unstructured information that requires flexibility. Researchers can use an ELN (such as {% tool "elabftw" %}) in a personalised way and adapt it to document their everyday work.
 
-  * Laboratory Information Management Systems (LIMS) typically follow pre-defined and highly structured experimental workflow. LIMS are used to document and track biological samples through the experimental processes and can support direct import of data from sources such as instruments.
+  * Laboratory Information Management Systems (LIMS) typically follow pre-defined and highly structured experimental workflow. LIMS are used to document and track biological samples through the experimental processes and can support direct import of data from sources such as instruments (e.g {% tool "labid" %}).
 
   * Electronic Data Capture (EDC) systems are usually designated for collection of clinical trial data.