W4M lab - add contents

Author: lecorguille

communities/workflow4metabolomics/lab/base.yml

@@ -15,7 +15,7 @@ nationality: European
 # Used for rendering tool/workflow links. Trailing '/' will be removed.
 galaxy_base_url: https://workflow4metabolomics.usegalaxy.fr
 subdomain: workflow4metabolomics
-root_domain: usegalaxy.eu
+root_domain: usegalaxy.fr
 support_url: https://help.galaxyproject.org/
 general_support: https://galaxyproject.org/support/
 figure_workflow4metabolomics_url: https://ifb-elixirfr.gitlab.io/usegalaxy-fr/welcome//workflow4metabolomics/images/workflow_w4m_HD.png
@@ -62,5 +62,6 @@ sections:
   - sections/3_GCMS.yml
   - sections/4_FIAMS.yml
   - sections/5_NMR.yml
+  - sections/9_citations.yml
 
 # -----------------------------------------------------------------------------

communities/workflow4metabolomics/lab/sections/1_data_import_and_preparation.yml

@@ -38,15 +38,18 @@ tabs:
           What is Galaxy?
         button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/introduction/slides.html
         button_tip: Open Learning Pathway
+        button_icon: view
       - title_md: Galaxy Basics for everyone
         description_md: >
           This practical aims at familiarizing you with the Galaxy user interface. It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows and sharing your work. 
         button_link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/tutorial.html
         button_tip: Open Learning Pathway
+        button_icon: run
       - title_md: Introduction to Metabolomics
         description_md: >
           The presentation will introduce you to the field of metabolomics, its applications, and the tools available in Galaxy for metabolomics data analysis.
         button_link: https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/introduction/slides.html
         button_tip: Open Learning Pathway
+        button_icon: view
 
 

communities/workflow4metabolomics/lab/sections/2_LCMS.yml

@@ -24,7 +24,7 @@ tabs:
     button_link: 
       https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/slides.html
     button_tip: View slides
-    button_icon: tutorial
+    button_icon: view
   - title_md: "Mass spectrometry: LC-MS preprocessing with XCMS"
     description_md: >
       This tutorial will guide you through the steps of processing LC-MS data in Galaxy, including data import, quality control, and feature detection.

communities/workflow4metabolomics/lab/sections/3_GCMS.yml

@@ -8,7 +8,7 @@ tabs:
   title: Workflows
   heading_md: ""
   content:
-    - title_md: "gcms-metams"
+    - title_md: "GC/MS metaMS data processing"
       description_md: >
         This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.
       button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=680'

communities/workflow4metabolomics/lab/sections/9_citations.yml

@@ -0,0 +1,96 @@
+id: citations
+title: Cite Us and Acknowledgements
+tabs:
+  - id: citations
+    title: Cite Us
+    heading_md: >
+      Please cite the following papers when using this tool:
+    content:
+      - title_md: Galaxy Project Primary Publication
+        description_md: >
+          The Galaxy Community. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024;, gkae410, https://doi.org/10.1093/nar/gkae410
+        button_link: "https://doi.org/10.1093/nar/gkae410"
+        button_tip: Access paper
+        button_icon: view
+      - title_md: "Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics"
+        description_md: >
+          Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics. doi:10.1093/bioinformatics/btu813
+        button_link: "https://doi.org/10.1093/bioinformatics/btu813"
+        button_tip: Access paper
+        button_icon: view
+      - title_md: Create, Run, Share, Publish, and Reference Your LC–MS, FIA–MS, GC–MS, and NMR Data Analysis Workflows with the Workflow4Metabolomics 3.0 Galaxy Online Infrastructure for Metabolomics.
+        description_md: >
+          Guitton, Yann, Marie Tremblay-Franco, Gildas Le Corguillé, Jean-François Martin, Mélanie Pétéra, Pierrick Roger-Mele, Alexis Delabrière, et al. 2017. “Create, Run, Share, Publish, and Reference Your LC–MS, FIA–MS, GC–MS, and NMR Data Analysis Workflows with the Workflow4Metabolomics 3.0 Galaxy Online Infrastructure for Metabolomics.” The International Journal of Biochemistry & Cell Biology 93: 89–101. doi.org/10.1016/j.biocel.2017.07.002
+        button_link: "https://doi.org/10.1016/j.biocel.2017.07.002"
+        button_tip: Access paper
+        button_icon: view
+  - id: acknowledgements
+    title: Acknowledgements
+    heading_md: >
+      Acknowledgements for the Workflow4Metabolomics supports when using this tool
+    content:
+      - title_md: "IFB Core Cluster: RENABI and MUDIS4LS funding"
+        description_md: >
+          We thank the IFB Core Cluster computing resource which has benefited from State aid managed by the Agence Nationale de la Recherche under the France 2030 programme for the Institut Français de Bioinformatique (IFB), founded by the Programme d'Investissements d'Avenir, number ANR-11-INBS-0013, as well as structuring equipment for research / EQUIPEX+ bearing the reference ANR-21-ESRE-0048.
+      - title_md: MetaboHub
+        description_md: >
+          We thank the Workflow4Metabolomics project, which is part of the French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr) and funded by the ANR (MetaboHUB-ANR-11-INBS-0010).
+  - id: funders
+    title: Funders
+    heading_md: >
+      Funders for the Workflow4Metabolomics project
+    content:
+      - title_md: "France 2030"
+        description_md: >
+          The [IFB (French Institute of Bioinformatics)](https://www.france-bioinformatique.fr/en/home/) and [MetaboHub](https://www.metabohub.fr/home.html) are supported by the France 2030 programme.
+      - title_md: "Brittany / Bretagne Region"
+        description_md: >
+          The ABiMS IFB platform is supported by the Brittany / Bretagne Region via [BioGenouest](https://www.biogenouest.org/en/).
+      - title_md: "Auvergne-Rhône-Alpes Region"
+        description_md: >
+          The PEFM platform is supported by the Auvergne-Rhône-Alpes Region.
+  - id: affiliations
+    title: Affiliations
+    heading_md: >
+      Affiliations of the Workflow4Metabolomics contributors' teams
+    content:
+      - title_md: "[CNRS - French National Centre for Scientific Research](https://www.cnrs.fr/en)"
+        description_md: >
+          Teams:
+          <ul>
+              <li>[IFB Core](https://www.france-bioinformatique.fr/en/organisation-governance/operational-cells/hub-ifb-core/) - Ivry-sur-Seine - France</li>
+              <li>[ABiMS](https://www.abims.fr/) (IFB) - [Station Biologique de Roscoff](https://www.sb-roscoff.fr/en), France</li>
+          </ul>
+      - title_md: "[INRAE - National Institute of Agricultural Research](https://www.inrae.fr/en)"
+        description_md: >
+          <ul>
+              <li>PEFM (MetaboHub) - Clermont-Ferrand, France</li>
+              <li>MetaToul-AXIOM (MetaboHub), Toxalim - Toulouse, France</li>
+              <li>[LABERCA](https://www.laberca.fr/) (Laboratoire d’Etude des Résidus et Contaminants dans les Aliments), ONIRIS (MetaboHub) - Nantes, France</li>
+          </ul>
+      - title_md: "[CEA - French Alternative Energies and Atomic Energy Commission](https://www.cea.fr/english)"
+        description_md: >
+          Team:
+          <ul>
+            <li>[LIST Laboratory for Data Analysis and Smart Systems](https://list.cea.fr/en/) (MetaboHub) - Saclay, France</li>
+          </ul>
+      - title_md: "[Université Libre de Bruxelles](https://www.ulb.be/en)"
+        description_md: >
+          <ul>
+              <li>[RD3 - Pharmacognosy, Bioanalysis & Drug Discovery Unit](https://pharmacie.ulb.be/version-francaise/la-recherche/les-unites-de-recherche/pharmacognosie-bioanalyse-et-medicaments-pbm/pharmacognosie-bioanalyse-et-medicaments-pbm) - Brussels, Belgium</li>
+          </ul>
+      - title_md: "[Sorbonne Université](https://www.sorbonne-universite.fr/en)"
+        description_md: >
+          <ul>
+              <li>[ABiMS](https://www.abims.fr/) (IFB) - [Station Biologique de Roscoff](https://www.sb-roscoff.fr/en), France</li>
+          </ul>
+      - title_md: "[University of Birmingham](https://www.birmingham.ac.uk)"
+        description_md: >
+          <ul>
+            <li>[Data Science and Computational Metabolomics](https://www.birmingham.ac.uk) - Birmingham, UK</li>
+          </ul>
+      - title_md: "[Masaryk University](https://www.muni.cz/en)"
+        description_md: >
+          <ul>
+              <li>[RECETOX](https://www.recetox.muni.cz/en) - Brno, Czech Republic</li>
+          </ul>

communities/workflow4metabolomics/lab/static/elixir_france-logo.png

@@ -0,0 +1,17 @@
+<section class="my-5" id="tagline">
+
+    <div class="container">
+      <h5>Hosted by:</h5>
+      <div class="row align-items-center">
+        <div class="col-sm">
+          <a href="https://www.france-bioinformatique.fr/en/ifb-core-cluster/" target="_blank"><center><img src="https://www.france-bioinformatique.fr/wp-content/uploads/logo-ifb-couleur.svg" style="width:150px;" /></center></a>
+        </div>
+        <div class="col-sm">
+          <a href="https://elixir-europe.org/about-us/who-we-are/nodes/france" target="_blank"><center><img src="https://elixir-europe.org/sites/default/files/elixir_node_france_0.png" style="width:150px;" /></center></a>
+        </div>
+        <div class="col-sm">
+          <a href="https://www.economie.gouv.fr/france-2030" target="_blank"><center><img src="https://www.info.gouv.fr/upload/media/organization/0001/01/sites_default_files_contenu_illustration_2022_03_logotype-rouge-bleu.jpg" style="width:150px;" /></center></a>
+        </div>
+    </div>
+
+</section>