e-biogenouest : The Tools

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e-Biogenouest : The Tools

Coordinateur : Olivier Collin

Animateur : Yvan Le Bras

CNRS UMR 6074 IRISA-INRIA / Plateforme de Bioinformatique GenOuest

[email protected]

Programme fédérateur Biogenouest co-financé

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Infrastructure Project Management Education Tools Local Data & Metadata External Data

Software & e-Science

Besoins

Des données, des outils, des formations, une

infrastructure …

Workflows Scripts Softwares Talks Tutorials Courses Collaborators Goal / Description

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Software & e-Science

Caractère distribué, pas de point central…

… n’empêche pas un guichet unique!

Environnement de recherche virtuel

Collaboration

Portail

WEB

Données Logiciels Ressources de traitement Utilisateurs

Communauté

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GO4Bioinformatics

Software & e-Science

Caractère distribué, pas de point central…

… n’empêche pas un guichet unique!

Environnement de recherche virtuel

HUBzero

EMME / BIOMAJ GALAXY / Mobyle ReNaBiGO Utilisateurs

Communauté

Collaboration

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What is Science?

Shared data Analyse data Manage the data Simulate experiment observe Publication Research process Proposal writing Partners Ideas

Research

Lifecycle

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What is Science Today?

Searching Exploring Uploading Computing Visualizing Analysing Publishing Reviewing Questionning Discussing Collaborating Shared data Analyse data Manage the data Simulate experiment observe Publication Research process Proposal writing Partners Ideas

Research

Lifecycle

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What is e-Science?

Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating

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What can be the beginning of e-Science?

Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating Education

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HUBzero

Education Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating

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Galaxy / Mobyle

Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating Education

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EMME

Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating Education

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GO4Bioinformatics

Education Searching Exploring Uploading Computing Visualizing Analysing Verifying Publishing Reviewing Questionning Discussing Collaborating

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All-in Global schema

International & National

Dtata Banks

Institutional

Data Banks

eBGO

Data bank

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

Data & Metadata management

EMME Portal

-ISAtab format & archives -Browse & view metadata -Links towards: ISArchives Data Data analysis Galaxy as a bridge -Histories -Workflows -Visualization -Pages -Data Management

Private data (shared, public) Data librairies (public, private) Galaxy as a gate

-HPC resources -Tools & Methods

No Data centered

research processes

Data centered

research processes

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All-in Domain Specific : Bio-Imaging

International & National

Dtata Banks

Institutional

Data Banks

eBGO

Data bank

Data & Metadata management EMME Portal + OMERO Portal -automatic metadata extraction

-browse & view

Data analysis Galaxy -Histories -Workflows -Visualization -Pages -Data Management

Private data (shared, public) Data librairies (public, private) OMERO -Analysis Icy -bioimage analysis

No Data centered

research processes

Data centered

research processes

HUBzero as a gate

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All-in Domain Specific : Geographical data

International & National

Dtata Banks

Institutional

Data Banks

eBGO

Data bank

Data & Metadata management OpenGIS Web Processing + GeoServer Geomajas INSPIRE Data analysis Galaxy -Histories -Workflows -Visualization -Pages -Data Management

Private data (shared, public) Data librairies (public, private) GeoNetwork -Analysis

No Data centered

research processes

Data centered

research processes

HUBzero as a gate

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eBGO HUB : The GenOuest Example

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

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eBGO HUB : 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

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eBGO HUB : The GUGGO Example

1 public project : « Toolshed 4 GO »

17 members

1 public project : « Contribute 2 Galaxy »

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eBGO HUB : The Ectocyc Example

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?

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eBGO HUB : The Ectocyc Example

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

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It’s your Virtual Research Environment

Merci de votre attention….

Coordinateur : Olivier Collin Animateur : Yvan Le Bras CNRS UMR 6074 IRISA-INRIA / Plateforme de Bio-informatique GenOuest

[email protected]

HUB du projet http://www.e-biogenouest.org/

Portail EMME http://emme.genouest.org/

Instance Galaxy http://galaxy.genouest.org/