Merge pull request #6 from jsaintvanne/sd_update

updated galaxyW4M and added references in bibtex format

Workflow4Metabolomics Galaxy Documentation/galaxyW4M.qmd

@@ -1,24 +1,42 @@
 ---
   title: "What is Galaxy W4M ?"
+  bibliography: references.bib
 ---
 
 ## Our project 
 
-The Workflow4Metabolomics, W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
+The
+![](/images/Workflow4Metabolomic_icon.svg){height=1em}, ![](/images/W4M_icon.svg){height=1em} in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
 
-In the context of collaboration between metabolomics (MetaboHUB French infrastructure) and bioinformatics platforms (IFB: Institut Français de Bioinformatique), we have developed full LC/MS, GC/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis and annotation steps. Those modular and extensible workflows are composed with existing components (XCMS and CAMERA packages, etc.) but also a whole suite of complementary homemade tools. This implementation is accessible through a web interface, which guarantees the parameters completeness. The advanced features of Galaxy have made possible the integration of components from different sources and of different types. Thus, an extensible Virtual Research Environment (VRE) is offered to metabolomics communities (platforms, end users, etc.), and enables preconfigured workflows sharing for new users, but also experts in the field.
+In a collaborative efforts between metabolomics (
+[![](https://www.metabohub.fr/media/752){height=1.5em}](https://www.metabohub.fr/) French infrastructure
+) and bioinformatics platforms (
+[![](https://www.france-bioinformatique.fr/wp-content/uploads/logo-ifb-couleur.svg){height=1.5em}](https://www.france-bioinformatique.fr/) Institut Français de Bioinformatique
+), we've crafted comprehensive LC/MS, GC/MS, and NMR pipelines using the robust
+[![](https://galaxyproject.org/images/galaxy-logos/galaxy_logo_25percent.png){height=1em}](https://galaxyproject.org/)
+framework.
+Our **pipelines** cover the entire spectrum of data analysis, encompassing **preprocessing**, **normalization**, **quality control**, **statistical analysis**, and **annotation** steps.
 
-## Galaxy
+These modular and adaptable workflows are carefully assembled with a combination of established components (such as
+[XCMS](https://github.com/sneumann/xcms)
+and
+[CAMERA](https://github.com/sneumann/CAMERA)
+packages) and a suite of tools developed by the ![](/images/W4M_icon.svg){height=1em} team members. Our implementation, accessible through a user-friendly web interface, ensures the completeness of parameter settings and reproducibility. Leveraging the advanced capabilities of 
+[![](https://galaxyproject.org/images/galaxy-logos/galaxy_logo_25percent.png){height=1em}](https://galaxyproject.org/)
+, we seamlessly integrate components from diverse sources and types.
+
+This integration has facilitated the creation of an extensible Virtual Research Environment (VRE) tailored for metabolomics communities, including platforms and end-users. Our VRE offers preconfigured workflows for newcomers while catering to experts in the field. This collaborative approach not only ensures accessibility but also encourages knowledge-sharing and enhances the overall research experience.
 
-Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
 
-Homepage: [https://galaxyproject.org/](https://galaxyproject.org/)
+## Galaxy
 
-workflow
+[![](https://galaxyproject.org/images/galaxy-logos/galaxy_logo_25percent.png){height=1em}](https://galaxyproject.org/) is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
 
 
 ## Citation
 
-Giacomoni F., Le Corguillé G., Monsoor M., Landi M., Pericard P., Pétéra M., Duperier C., Tremblay-Franco M., Martin J.-F., Jacob D., Goulitquer S., Thévenot E.A. and Caron C. (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics, http://dx.doi.org/10.1093/bioinformatics/btu813
+@GUITTON201789
+
+@GIACOMONI201412
+
 
-Guitton Y., Tremblay-Franco M., Le Corguillé G., Martin J.F., Pétéra M., Roger-Mele P., Delabrière A., Goulitquer S., Monsoor M., Duperier C., Canlet C., Servien R., Tardivel P., Caron C., Giacomoni F., Thévenot E.A., 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, 2017, ISSN 1357-2725, http://dx.doi.org/10.1016/j.biocel.2017.07.002. This paper is also available on the open archive HAL.

Workflow4Metabolomics Galaxy Documentation/index.qmd

@@ -29,6 +29,7 @@ You can subscribe to [our newsletter](https://groupes.france-bioinformatique.fr/
 
 ### Resources
 
+
 **I'm a newcomer** and I want to know more about ![](/images/W4M_icon.svg){height=1em}, visit our [about us](about.qmd) section
 
 **I want to learn** how to **process metabolomics data**, you can either:

Workflow4Metabolomics Galaxy Documentation/references.bib

@@ -0,0 +1,29 @@
+@article{GIACOMONI201412,
+    author = {Giacomoni, Franck and Le Corguillé, Gildas and Monsoor, Misharl and Landi, Marion and Pericard, Pierre and Pétéra, Mélanie and Duperier, Christophe and Tremblay-Franco, Marie and Martin, Jean-François and Jacob, Daniel and Goulitquer, Sophie and Thévenot, Etienne A. and Caron, Christophe},
+    title = "{Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics}",
+    journal = {Bioinformatics},
+    volume = {31},
+    number = {9},
+    pages = {1493-1495},
+    year = {2014},
+    month = {12},
+    abstract = "{Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation.Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure.W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB).Contact  :  [email protected]}",
+    issn = {1367-4803},
+    doi = {10.1093/bioinformatics/btu813},
+    url = {https://doi.org/10.1093/bioinformatics/btu813},
+    eprint = {https://academic.oup.com/bioinformatics/article-pdf/31/9/1493/50306491/bioinformatics\_31\_9\_1493.pdf},
+}
+
+@article{GUITTON201789,
+title = {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},
+journal = {The International Journal of Biochemistry & Cell Biology},
+volume = {93},
+pages = {89-101},
+year = {2017},
+issn = {1357-2725},
+doi = {https://doi.org/10.1016/j.biocel.2017.07.002},
+url = {https://www.sciencedirect.com/science/article/pii/S1357272517301577},
+author = {Yann Guitton and Marie Tremblay-Franco and Gildas {Le Corguillé} and Jean-François Martin and Mélanie Pétéra and Pierrick Roger-Mele and Alexis Delabrière and Sophie Goulitquer and Misharl Monsoor and Christophe Duperier and Cécile Canlet and Rémi Servien and Patrick Tardivel and Christophe Caron and Franck Giacomoni and Etienne A. Thévenot},
+keywords = {Metabolomics, Data analysis, E-infrastructure, Workflow, Galaxy, Repository},
+abstract = {Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC–MS, FIA–MS, GC–MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows.}
+}