diff --git a/Workflow4Metabolomics Galaxy Documentation/W4M_datasets/sacurine.qmd b/Workflow4Metabolomics Galaxy Documentation/W4M_datasets/sacurine.qmd new file mode 100644 index 0000000..43a7ddb --- /dev/null +++ b/Workflow4Metabolomics Galaxy Documentation/W4M_datasets/sacurine.qmd @@ -0,0 +1,24 @@ +--- +title: "Sacurine" +doi: "[publication](https://pubs.acs.org/doi/10.1021/acs.jproteome.5b00354)" +# history: "[W4M00001_Sacurine-statistics](https://workflow4metabolomics.usegalaxy.fr/published/history?id=3052e053b71f3ff5)" +uthor: "Thevenot et al." +description: "Analysis of the human adult urinary metabolome" +bibliography: "../references.bib" +galaxyref: "W4M00001" +link: "[MTBLS404](https://www.ebi.ac.uk/metabolights/editor/MTBLS404/descriptors)" +--- + +## Description + +**Study:** +Characterization of the physiological variations of the metabolome in biofluids is critical to understand human physiology and to avoid confounding effects in cohort studies aiming at biomarker discovery. + +**Dataset:** +In this study conducted by the MetaboHUB French Infrastructure for Metabolomics, urine samples from 184 volunteers were analyzed by reversed-phase (C18) ultrahigh performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (LTQ-Orbitrap). A total of 258 metabolites were identified at confidence levels provided by the metabolomics standards initiative (MSI) levels 1 or 2. + +**Workflow:** +This history describes the statistical analysis of the data set from the negative ionization mode (113 identified metabolites at MSI levels 1 or 2): correction of signal drift (loess model built on QC pools) and batch effects (two batches), variable filtering (QC coefficent of variation < 30%), normalization by the sample osmolality, log10 transformation, sample filtering (Hotelling, decile and missing pvalues > 0.001) resulting in the HU_096 sample being discarded, univariate hypothesis testing of significant variations with age, BMI, or between genders (FDR < 0.05), and OPLS(-DA) modeling of age, BMI and gender. + +**Comments:** +The ‘sacurine’ data set (after normalization and filtering) is also available in the ropls R package from the Bioconductor repository. For a comprehensive analysis of the dataset (starting from the preprocessing of the raw files and including all detected features in the subsequent steps), please see the companion ‘W4M00002_Sacurine-comprehensive’ reference history. \ No newline at end of file diff --git a/Workflow4Metabolomics Galaxy Documentation/_quarto.yml b/Workflow4Metabolomics Galaxy Documentation/_quarto.yml index 0617e27..2bccfb1 100644 --- a/Workflow4Metabolomics Galaxy Documentation/_quarto.yml +++ b/Workflow4Metabolomics Galaxy Documentation/_quarto.yml @@ -27,16 +27,18 @@ website: - text: "Galaxy W4M" icon: "boxes" menu: - - text: "Autre chose" + - text: "Introduction" href: galaxyW4M.qmd - - text: "Encore autre chose" - href: galaxyW4M.qmd - - text: "Tool development" + icon: "info-circle" + - text: "Guides for Users" + href: tooluser.qmd + icon: "code" + - text: "Guides for Developpers" href: tooldev.qmd - icon: "pencil-square" - - text: "I want to contribute" + icon: "code" + - text: "How to contribute" href: contribute.qmd - icon: "pencil-square" + icon: "person-fill-up" - text: "Tools" icon: "tools" menu: diff --git a/Workflow4Metabolomics Galaxy Documentation/galaxyW4M.qmd b/Workflow4Metabolomics Galaxy Documentation/galaxyW4M.qmd index ffffb33..0d663b9 100644 --- a/Workflow4Metabolomics Galaxy Documentation/galaxyW4M.qmd +++ b/Workflow4Metabolomics Galaxy Documentation/galaxyW4M.qmd @@ -1,24 +1,49 @@ --- 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 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. + +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. -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. ## Galaxy -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. +[![](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. -Homepage: [https://galaxyproject.org/](https://galaxyproject.org/) +The main features of this platform are: -workflow +* A real benefit to users with results traceability and storage +* The ability to share results between users/labs/platforms +* The possibility to use a complete analysis workflow managing environment +* Interactive step-by-step tutorials called [![](https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png){height=1em} Galaxy training](https://training.galaxyproject.org/training-material/topics/metabolomics/) ## 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. diff --git a/Workflow4Metabolomics Galaxy Documentation/images/W4E_icon.svg b/Workflow4Metabolomics Galaxy Documentation/images/W4E_icon.svg index 0972854..03dc738 100644 --- a/Workflow4Metabolomics Galaxy Documentation/images/W4E_icon.svg +++ b/Workflow4Metabolomics Galaxy Documentation/images/W4E_icon.svg @@ -9,11 +9,11 @@ id="svg1" inkscape:version="1.3.2 (091e20e, 2023-11-25, custom)" sodipodi:docname="W4E_icon.svg" + xml:space="preserve" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns="http://www.w3.org/2000/svg" - xmlns:svg="http://www.w3.org/2000/svg"> - - - - - W - WE - E4 - - - + y="22.998728">4 diff --git a/Workflow4Metabolomics Galaxy Documentation/images/W4M_icon.svg b/Workflow4Metabolomics Galaxy Documentation/images/W4M_icon.svg index bc68fb6..f960c7a 100644 --- a/Workflow4Metabolomics Galaxy Documentation/images/W4M_icon.svg +++ b/Workflow4Metabolomics Galaxy Documentation/images/W4M_icon.svg @@ -24,7 +24,7 @@ inkscape:deskcolor="#d1d1d1" inkscape:document-units="mm" inkscape:zoom="2.9255612" - inkscape:cx="64.261176" + inkscape:cx="64.60299" inkscape:cy="15.552572" inkscape:window-width="1920" inkscape:window-height="1017" @@ -44,24 +44,24 @@ transform="matrix(1.2870299,0,0,1.2870299,-5.0830531,-5.5074213)"> W M + + + + + + + + Workflow + Metabolomics + 4 + + + diff --git a/Workflow4Metabolomics Galaxy Documentation/index.qmd b/Workflow4Metabolomics Galaxy Documentation/index.qmd index 81dfbeb..d6b45f0 100644 --- a/Workflow4Metabolomics Galaxy Documentation/index.qmd +++ b/Workflow4Metabolomics Galaxy Documentation/index.qmd @@ -29,12 +29,14 @@ 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: * Go to our teaching school event [![](/images/W4E_icon.svg){height=1em} section](TODO) -* Consult our official [Galaxy training guides ![](https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png){height=1em}](https://training.galaxyproject.org/training-material/topics/metabolomics/) +* Consult our [user page here](tooluser.qmd) +* Or directly go to our official [Galaxy training guides ![](https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png){height=1em}](https://training.galaxyproject.org/training-material/topics/metabolomics/) **I want to contribute as:** diff --git a/Workflow4Metabolomics Galaxy Documentation/references.bib b/Workflow4Metabolomics Galaxy Documentation/references.bib new file mode 100644 index 0000000..6569023 --- /dev/null +++ b/Workflow4Metabolomics Galaxy Documentation/references.bib @@ -0,0 +1,58 @@ +@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  :  contact@workflow4metabolomics.org}", + 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.} +} + +@article{HILTEMANN202301, + doi = {10.1371/journal.pcbi.1010752}, + url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752}, + year = 2023, + month = {jan}, + publisher = {Public Library of Science ({PLoS})}, + volume = {19}, + number = {1}, + pages = {e1010752}, + author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and}, + editor = {Francis Ouellette}, + title = {Galaxy Training: A powerful framework for teaching!}, + journal = {PLoS Comput Biol Computational Biology} +} + +@article{THEVENOT_2015, + author = {Thévenot, Etienne A. and Roux, Aurélie and Xu, Ying and Ezan, Eric and Junot, Christophe}, + title = {Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses}, + journal = {Journal of Proteome Research}, + volume = {14}, + number = {8}, + pages = {3322-3335}, + year = {2015}, + doi = {10.1021/acs.jproteome.5b00354}, + note ={PMID: 26088811}, + URL = {https://doi.org/10.1021/acs.jproteome.5b00354}, + eprint = {https://doi.org/10.1021/acs.jproteome.5b00354} +} \ No newline at end of file diff --git a/Workflow4Metabolomics Galaxy Documentation/ressources/Help_template.txt b/Workflow4Metabolomics Galaxy Documentation/ressources/Help_template.txt new file mode 100644 index 0000000..9d25e04 --- /dev/null +++ b/Workflow4Metabolomics Galaxy Documentation/ressources/Help_template.txt @@ -0,0 +1,163 @@ + \ No newline at end of file diff --git a/Workflow4Metabolomics Galaxy Documentation/tooldev.qmd b/Workflow4Metabolomics Galaxy Documentation/tooldev.qmd index 98a2811..515caec 100644 --- a/Workflow4Metabolomics Galaxy Documentation/tooldev.qmd +++ b/Workflow4Metabolomics Galaxy Documentation/tooldev.qmd @@ -44,5 +44,8 @@ Among the possible variations for functional XML wrappers, W4M is willing to gar **TODO** Topo sur l'importance de la doc -**TODO** Lien vers le template-type +**TODO** Presenter les section mandatory et facultative + +About the format, you can find [here](ressources/Help_template.txt) +a template of Help tag to help you initiating your writing with the recommanded sections and formats. diff --git a/Workflow4Metabolomics Galaxy Documentation/tooluser.qmd b/Workflow4Metabolomics Galaxy Documentation/tooluser.qmd new file mode 100644 index 0000000..f15e43a --- /dev/null +++ b/Workflow4Metabolomics Galaxy Documentation/tooluser.qmd @@ -0,0 +1,41 @@ +--- + title: "User guide" + listing: + - id: list_W4M_datasets + contents: "W4M_datasets/*.qmd" + type: table + sort: "date" + max-items: 100 + fields: [galaxyref, link, title, author, history, doi] +--- + +The most effective way to master the use of our tools is by enrolling in our comprehensive training school ![](/images/W4E_icon.svg){height=1em}. Below you will find in-depth learning guides, providing you with the skills you need to leverage our tools seamlessly. + +## Galaxy Training Network on Metabolomics + +Access complete and interactive step-by-step guides by visiting the [![](https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png){height=1em} Galaxy Training Network on metabolomics](https://training.galaxyproject.org/training-material/topics/metabolomics/). + +```{=html} + +``` + +## Galaxy ![](/images/W4M_icon.svg){height=1em} Instance + +Explore our [![](https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo_square.png){height=2em} Galaxy instance](https://workflow4metabolomics.usegalaxy.fr/) were each tool is accompanied by comprehensive support, including helpful documentation, examples, and references, ensuring that you have the resources you need. + +## Workflows examples + + + +## Datasets examples + + +:::{#list_W4M_datasets} + +::: \ No newline at end of file