e-biogenouest : The Tools Coordinateur : Olivier Collin Animateur : Yvan Le Bras CNRS UMR 6074 IRISA-INRIA / Plateforme de Bioinformatique GenOuest yvan.le_bras@irisa.fr Programme fédérateur Biogenouest co-financé 24 mois
Software & e-science Besoins Des données, des outils, des formations, une infrastructure External Data Courses Local Data & Metadata Education Tutorials Talks Softwares Scripts Tools Workflows Infrastructure Project Management Goal / Description Collaborators Working groups
Software & e-science Caractère distribué, pas de point central n empêche pas un guichet unique! Environnement de recherche virtuel Données Collaboration Utilisateurs Portail WEB Logiciels Communauté Ressources de traitement
Software & e-science Caractère distribué, pas de point central n empêche pas un guichet unique! Environnement de recherche virtuel EMME / Collaboration BIOMAJ Utilisateurs HUBzero GO4Bioinformatics GALAXY / Mobyle Communauté ReNaBiGO
WhatisScience? Ideas Partners Publication Research Lifecycle Proposal writing Research process Shared data Simulate experiment observe Analyse data Manage the data
WhatisScience Today? Searching Collaborating Ideas Exploring Discussing Publication Research Lifecycle Partners Uploading Questionning Proposal writing Computing Research process Reviewing Shared data Simulate experiment observe Visualizing Publishing Analyse data Manage the data Analysing Verifying
Whatise-Science? Searching Collaborating Exploring Discussing Uploading Questionning Computing Reviewing Visualizing Publishing Analysing Verifying
Whatcanbethe beginningof e-science? Searching Collaborating Exploring Discussing Uploading Questionning Education Computing Reviewing Visualizing Publishing Verifying Analysing
HUBzero Collaborating Searching Exploring Discussing Uploading Questionning Education Computing Reviewing Visualizing Publishing Verifying Analysing
Galaxy/ Mobyle Searching Collaborating Exploring Discussing Uploading Questionning Education Computing Reviewing Visualizing Publishing Verifying Analysing
EMME Collaborating Searching Exploring Discussing Uploading Questionning Education Computing Reviewing Visualizing Publishing Verifying Analysing
GO4Bioinformatics Searching Collaborating Exploring Discussing Uploading Questionning Education Computing Reviewing Visualizing Publishing Verifying Analysing
All-inGlobal schema Institutional Data Banks ebgo Data bank International & National Dtata Banks Project Management & Collaboration HUBzero as a bridge embedded links towards -tools/software -data -metadata -references HUBzero«alone» -User & Group Management -Wiki -Calendar -Resources -Training/Course -Multimedia Reference Manager -HAL -Zotero -CiteUlike -BioblioGO -Mendeley No Data centered research processes HUBzeroas a gate Data & Metadata management EMME Portal -ISAtab format & archives -Browse & view metadata -Links towards: ISArchives Data Data centered research processes Data analysis Galaxyas a bridge -Histories -Workflows -Visualization -Pages -Data Management Private data (shared, public) Data librairies (public, private) Galaxyas a gate -HPC resources -Tools & Methods
All-inDomain Specific: Bio-Imaging Institutional Data Banks ebgo Data bank International & National Dtata Banks Project Management & Collaboration HUBzero as a bridge embedded links towards -tools/software -data -metadata -references HUBzero«alone» -User & Group Management -Wiki -Calendar -Resources -Training/Course -Multimedia Reference Manager -HAL -Zotero -CiteUlike -BioblioGO -Mendeley No Data centered research processes HUBzeroas a gate Data & Metadata management EMME Portal + OMERO Portal -automatic metadata extraction -browse & view Data centered research processes Data analysis Galaxy -Histories -Workflows -Visualization -Pages -Data Management Private data (shared, public) Data librairies (public, private) OMERO -Analysis Icy -bioimage analysis
All-inDomain Specific: Geographicaldata Institutional Data Banks ebgo Data bank International & National Dtata Banks Project Management & Collaboration HUBzero as a bridge embedded links towards -tools/software -data -metadata -references HUBzero«alone» -User & Group Management -Wiki -Calendar -Resources -Training/Course -Multimedia Reference Manager -HAL -Zotero -CiteUlike -BioblioGO -Mendeley No Data centered research processes Data & Metadata management OpenGIS Web Processing + GeoServer Geomajas INSPIRE HUBzeroas a gate Data centered research processes Data analysis Galaxy -Histories -Workflows -Visualization -Pages -Data Management Private data (shared, public) Data librairies (public, private) GeoNetwork -Analysis
Our Life Sciences VRE proposal
ebgohub
ebgohub : The GenOuestExample 1 group : «GenOuest Core Facility» 12 members 1 wiki on Gitlab@Genouest 1 Wish for log creation Several projects ebiogenouest France Génomique Rapsodyn HUBzero test & development Mobyle2 Galaxy@Genouest
ebgohub : The GUGGO Example 1 restricted group : «GUGGO» 2 groups pages 17 members 2 wiki on Gitlab@Genouest 8 resources 2 discussions 2 Wish Calendar & events Several projects Galaxy@Genouest Toolshed 4 GO Contrib 2 Galaxy
ebgohub : The GUGGO Example 1 public project : «Toolshed 4 GO» 17 members 1 public project : «Contribute 2 Galaxy» 17 members
ebgohub : The EctocycExample EctoCyc consists in reconstructing the metabolic network of Ectocarpus Siliculosus This project aims to facilitate the collaboration between Dyliss team and The Roscoff Marine Station team. The EctoCyc projet Biologists / Bioinformaticians collaboration Manual verification of automatic reconstruction How to analyse the network? Did they use the same way to do it? How to share results? How to discuss about analyses & observations? How to keep track?
ebgohub : The EctocycExample 1 private group : «EctoCyc» 1 private project : «EctoCyc» 7 members One discussion group Html pages integration ebgo presentation at Roscoff Establishment of a working procedure Each scientis work differently Use of MS Excel & Word Use of the upload function To-do (7 ongoing & 15 off) Notes describe files content Each scientist manage analysis domain
It syourvirtual ResearchEnvironment Merci de votre attention. Coordinateur : Olivier Collin Animateur : Yvan Le Bras CNRS UMR 6074 IRISA-INRIA / Plateforme de Bio-informatique GenOuest yvan.le_bras@irisa.fr HUB du projet Portail EMME Instance Galaxy GO4Bioinformatics http://www.e-biogenouest.org/ http://emme.genouest.org/ http://galaxy.genouest.org/ http://go4bioinformatics.genouest.org/