Pasteur

Infrastructure
Propriétaire
Effective storage
2 200.00 To
Cluster: cores number
3 464 cores
Data collections number
76
CPU/hours a year
9 828 472 H / an
Bioinformatic tools number
5 980
Users number (last year)
302
Servers description

serveurs :

  • 2 noeuds (40 coeurs, 512GB RAM)
  • ​​52 noeuds (12 coeurs, 256GB RAM)
  • 225 noeuds (12 coeurs, 64GB RAM)
  • 1 noeud GPU-K80 (20 cores, 256 GB RAM, 4xNvidia-K80)
  • 2 noeuds GPU-M40 (20 cores, 256 GB RAM, 4xNvidia-M40)

stockage Isilon accessible via NFS

cluster géré via Sun Grid Engine (ou descendants) puis SLURM

programmes bioinformatiques accessible via « module » .

Le détail des données et outils est  accessible à l'adresse suivante:  https://bioweb.pasteur.fr/


Access conditions

accès restreint aux membres de l'Institut Pasteur.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
01-12-2016

Listeriomics : Systems Biology of Listeria

Description

Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format. Use Listeriomics for deciphering regulatory mechanisms of your genome element of interest.

Reference

Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
mSystems Mar 2017, 2 (2) e00186-16; DOI: 10.1128/mSystems.00186-16

Access conditions

freely accessible at http://listeriomics.pasteur.fr/

Annual visits:
8 085 an
Unique visits:
1 530 an
Quotes:
4
Latest update:
29-01-2016

MacSyDB/TXSSdb

Description

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane. They are also involved in complex antagonistic ecological interactions between bacteria. We designed models and protein profiles to detect an unprecedented number and diversity (∼10000) of bacterial protein secretion systems (T1SS, T2SS, T3SS, T4SS, T5SS, T6SSi-iii, T9SS) and evolutionarily related appendages (T4P, Tad, Flagellum) in 1528 genomes of diderm bacteria.

ref:

Abby, Sophie S., Jean Cury, Julien Guglielmini, Bertrand Néron, Marie Touchon, and Eduardo PC Rocha.

"Identification of protein secretion systems in bacterial genomes." Scientific reports 6 (2016).

Access conditions

freely accessible at http://macsydb.web.pasteur.fr/

No website documented
Annual visits:
831 013 an
Unique visits:
95 031 an
Quotes:
4
Latest update:
07-01-2015

Genolist servers

Description

There are 17 Genolist servers, each server is dedicated to a particular organism. The Genolist servers integrate informations about genome from different origins.
These servers allow to browse genomes against several criteria, and visualized the information in its genetic context.
The Genolist servers are followings :

 

SubtiList : Bacillus subtilis strain 168 GenoList browser
Colibri : Escherichia coli strain K12 GenoList browser
TubercuList : Mycobacterium tuberculosis strain H37Rv GenoList browser
Leproma : Mycobacterium leprae strain TN GenoList browser
BoviList : Mycobacterium bovis strain AF2122/97 GenoList browser
BuruList : Mycobacterium ulcerans strain Agy99 GenoList browser
ListiList : Listeria monocytogenes strain EGD-e and Listeria innocua strain CLIP 11262 Multi-GenoList browser
LegioList : Legionella pneumophila Paris strain and Legionella pneumophila Lens strain Multi-GenoList browser
PyloriGene : Helicobacter pylori strains 26694 and J99 Multi-GenoList browser
MypuList : Mycoplasma pulmonis strain UAB CTIP GenoList browser
CyanoList : Synechocystis PCC6803 and Anabaena PCC7120 Multi-GenoList browser
AureoList : Staphylococcus aureus strains N315 and Mu50 Multi-GenoList browser
StreptoPneumoList : Streptococcus pneumoniae strains R6 and Tigr4 Multi-GenoList browser
SagaList : Streptococcus agalactiae strain NEM316 GenoList browser
PhotoList : Photorhabdus luminescens strain TT01 GenoList browser
CandidaDB : Candida albicans strain SC5314 GenoList browser

Access conditions

Accès libre

No website documented
Annual visits:
809 287 an
Unique visits:
145 an
Quotes:
13
Latest update:
22-01-2014

Multi-Genome Genolist

Description

GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtractive genome analysis and dynamic synteny visualization.

Access conditions

accès libre

Annual visits:
8 529 an
Unique visits:
3 987 an
Quotes:
92
Latest update:
22-01-2014

secreton

Description

 

The http://secreton.web.pasteur.fr/ web site allows to query a dataset of 216 NF-T3SS retrieved from 1385 complete genome sequences. These systems were detected with proteic profiles of NF-T3SS core genes (sctC, sctN, sctJ, sctQ, sctR, sctS, sctT, sctU, sctV), and with an analysis of the genomic context of the hits obtained. This dataset along with the methodology is described in

Abby SS, Rocha EPC (2012) The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems. PLoS Genet 8(9): e1002983.

Access conditions

freely accessible at http://secreton.web.pasteur.fr

Annual visits:
14 936 an
Unique visits:
3 332 an
Quotes:
27
Latest update:
22-01-2014

Conjdb

Description

This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 mobilization systems retrieved from 2,269 complete genome sequences. These systems were detected with protein profiles of T4SS components, coupling proteins and relaxases. The hits were then filtered with a criterion of co-localization.

This dataset along with the methodology is described in

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Julien Guglielmini, Bertrand Néron, Sophie S. Abby, María Pilar Garcillán-Barcia, Fernando de la Cruz and Eduardo P. C. Rocha

Nucleic Acids Research, 2014 1

doi: 10.1093/nar/gku194 1

 

Access conditions

freely available at http://conjdb.web.pasteur.fr/

Annual visits:
1 855 an
Unique visits:
742 an
Quotes:
1
Downloads:
127

SHAMAN: a Shiny Application for Metagenomic ANalysis

Description

SHAMAN is a SHiny application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization.

SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, as suggested in [McMurdie and Holmes 2014, Jonsson2016] . SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [Love 2014] . Resulting p-values are adjusted according to the Benjamini and Hochberg procedure [Benjamini and Hochberg 1995]. The PCOA is performed with the ade4 R package and plots are generated with ggplot2 or D3.js packages .     

Access conditions

the web server is open and available at  http://shaman.c3bi.pasteur.fr/

the code is accessible here https://github.com/aghozlane/shaman and release under the GPLv3 license.

Annual visits:
1 524 an
Unique visits:
833 an
Quotes:
1
Downloads:
Not documented

MEMHDX

Description

MEMHDX allows users to perfom an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.

ref:

Véronique Hourdel, Stevenn Volant, Darragh P. O’Brien, Alexandre Chenal, Julia Chamot-Rooke, Marie-Agnès Dillies, Sébastien Brier; MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. Bioinformatics 2016; 32 (22): 3413-3419. doi: 10.1093/bioinformatics/btw420

Access conditions

MEMHDX is freely available as a web tool at http://memhdx.c3bi.pasteur.fr/

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
4
Downloads:
Not documented

SARTools

Description

SARTools is a R package dedicated to the differential analysis of RNA-seq data. It provides tools to generate descriptive and diagnostic graphs, to run the differential analysis with one of the well known DESeq2 or edgeR packages and to export the results into easily readable tab-delimited files. It also facilitates the generation of a HTML report which displays all the figures produced, explains the statistical methods and gives the results of the differential analysis.

Access conditions

https://github.com/PF2-pasteur-fr/SARTools

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

IntegronFinder

Description

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (galaxy), or by command line (IntegronFinder on github).

Integrons are major genetic element, notorious for their major implication in the spread of antibiotic resistance genes. More generally,  integrons are gene-capturing device, whose broader evolutionary role remains poorly understood. IntegronFinder is able to detect with high accuracy integron in DNA sequences. It is accurate because it combines the use of HMM profiles for the detection of the essential protein, the site-specific integron integrase, and the use of Covariance Models for the detection of the recombination site, the attC site.

IntegronFinder can also annotate gene cassettes (CDS nearby attC sites) using Resfams, a database of HMM profiles aiming at annotating antibiotic resistance genes. This database is provided but the user can add any other HMM profiles database of its own interest.

Access conditions

Integron_Finder is released under the GPLv3 license  and is available here: https://github.com/gem-pasteur/Integron_Finder

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

SynTView

Description

SynTView is a comparative and interactive viewer for microbial genomes, designed to run as either a web-based tool (Flash technology) or a desktop application (AIR environment). The basis of the program is a generic genome browser with sub-maps holding information about genomic objects (annotations). The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data (typically Single Nucleotide Polymorphisms — SNPs) along these genomes; these features are accessible to the user in an integrated way. A variety of specialised views are available and are all dynamically inter-connected (including linear and circular multi-genome representations, dot plots, phylogenetic profiles, SNP density maps, and more).

Documentation, tutorials and demonstration sites are available at the URL: http://genopole.pasteur.fr/SynTView

Access conditions
No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
2
Downloads:
Not documented

macsyfinder

Description

Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

MacSyFinder is a program to model and detect macromolecular systems, genetic pathways in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection.

Criteria for systems detection include component content (quorum), and genomic co-localization. Each component corresponds to a hidden Markov model (HMM) protein profile to perform homology searches with the program Hmmer .

 

Homepage : https://github.com/gem-pasteur/macsyfinder

Access conditions

freely available  (GPLv2)

Annual visits:
209 734 an
Unique visits:
20 399 an
Quotes:
239
Downloads:
Not documented

Mobyle

Description

Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks.

Mobyle is the successor of Pise and the RPBS server, previous systems that provided web environments to define and execute bioinformatics analyses.

Functionalities:

  • data reusability: the tagging of the user data facilitates the reuse of input values or results between different programs.
  • automatic data validation and format conversion: the description of the expected data and their format allows to verify and convert input values if necessary.
  • service discovery and workflow authoring assistance: services are provided through a searchable menu; furthermore, type compatibility mechanisms between results and potential program inputs let users either interactively pipe tasks or build complete workflows before to run them.

Based on extensive user studies, we developed the end-user interface as a Web Portal that provides a global and integrated view of all the elements needed to perform analyses, such as the available programs, the submitted jobs and the data of interest.

References:

Bertrand Néron, Hervé Ménager, Corinne Maufrais, Nicolas Joly, Julien Maupetit, Sébastien Letort, Sébastien Carrere, Pierre Tuffery, and Catherine Letondal
Mobyle: a new full web bioinformatics framework
Bioinformatics (2009); 25 (22): 3005-3011. doi:10.1093/bioinformatics/btp493. 

Access conditions

The Mobyle framework is developped under the GPLv2 license.

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

fqtools

Description

fqtools is a package which provides tools to handle efficiently files in FASTAQ format.

The following tools are provided :

fqduplicate : retrieve duplicated entries

fqextract : extract entries

fqquality : filter a file according to the quality

ftp://ftp.pasteur.fr/pub/gensoft/projects/

Access conditions

access : free (GPLv2)

Domains of activity
  • Biomedical
  • Biology
Keywords:
  • NGS data analysis
  • Methodology
  • Genome and transcriptome assembly
  • Read mapping
  • Genomics (DNA-seq)
  • Genome analysis
  • Structural and functional genome annotation
  • Transcriptomics (RNA-seq)
  • Differential gene expression analysis
  • Transcripts and transcript variants analysis
  • Variant calling
  • Panels (amplicons, captures)
  • Exomes
  • Whole genomes
  • Analysis of gene expression regulation
  • Chip-seq
  • Small and long non-coding RNAs
  • Methylation profiles
  • Chromatin accessibility
  • Chromosome conformation analysis
  • Metagenomics, metatranscriptomics
  • Sequence analysis
  • Sequence algorithmics
  • Sequence annotation
  • Machine learning
  • Structural bioinformatics
  • System biology
  • Descriptive statistics
  • Statistical tests
  • Regression
  • Multivariate analysis
  • Dimension reduction
  • Inferences and biological network analysis
  • Genetic statistics
  • Cartography
  • Gene expression QTL analysis
  • Tool integration
  • Interoperability
  • Interfaces, web portals
  • Workflows developments
  • Data
  • Data integration
  • Databases and information systems
  • Computing environments
  • Cluster
  • Parallelisation
  • Evolution and phylogeny
  • Molecular evolution
  • Phylogenomics
  • Supertrees et reconciliations
  • Selection detection
  • Comparative genomics
  • Comparison of functional and regulatory pathways
  • Genomics: Chips
  • DNA chips
  • RNA chips
  • Expression
  • Tiling
  • Proteomics

Formation professionnelle

Trainees:
12 trainees / year
Training time:
5 day(s) / year
Upcoming session :
14-11-2016

Introduction à la Phylogénie Moléculaire : CONCEPTS, METHODES ET OUTILS

Description

Le C3BI (Institut Pasteur) propose des cours pour acquérir les notions théoriques de phylogénie et maitriser les outils et logiciels.
Les cours d’”Introduction à la phylogénie moléculaire” sont ouverts à tous (inscription obligatoire pour les cours et travaux pratiques dans la limite des places disponibles).
Il est possible de ne s’inscrire que pour la partie théorique. Ces cours sont dispensés en langue française.

  • Lundi 14 Novembre (9h30-12h30): Présentation des principales banques de données et BLAST
  • Mardi 15 Novembre (9h30-11h00): Alignements Multiples
  • Mercredi 16 Novembre (9h30-11h00): Introduction à la Phylogénie
  • Jeudi 17 Novembre (9h30-11h00): Modèles d’évolution
  • Vendredi 18 Novembre (9h30-11h00): Approches par Maximum de Parcimonie
  • Lundi 21 Novembre (9h30-11h00): Méthodes de Distance
  • Mardi 22 Novembre (9h30-11h00): Méthodes de Vraisemblance
  • Mercredi 23 Novembre (13h30-15h00): Reconstruction Phylogénétique & Approches Bayésiennes
  • Jeudi 24 Novembre (9h30-11h00): Inférence des Forces Sélectives
  • Vendredi 25 Novembre (9h30-11h00): Choix des Méthodes et Interprétation

programme complet

inscription par mail à formation@pasteur.fr (avec le sujet “Phylogénie Moléculaire”) + formulaire

Access conditions

ouvert à tous (chercheur,ingénieur, étudiant) mais inscription obligatoire par mail à formation@pasteur.fr (avec le sujet “Phylogénie Moléculaire”) + formulaire

Trainees:
30 trainees / year
Training time:
3 day(s) / year
No upcoming session scheduled

Initiation à l'analyse de données avec R

Description

Le cours s’adresse à des personnes qui veulent apprendre ou ré-apprendre à utiliser les statistiques à bon escient pour leurs propres projets. L’objectif est de présenter et expliquer les principales notions de statistiques utiles pour décrire un jeu de données, en explorer les propriétés afin d’en tirer des conclusions robustes, utiliser à bon escient les méthodes les plus courantes (tests d’hypothèse, ACP, …) et savoir lire, interpréter (et éventuellement aborder d’un œil critique) les résultats présentés dans les publications. Nous utiliserons le moins possible le formalisme mathématique mais insisterons sur les propriétés des méthodes, leurs pré-requis, l’interprétation des résultats. Nous aborderons les notions d’analyse exploratoire, ACP, clustering, estimation, échantillonnage, régression, tests d’hypothèse, planification d’expérience

Ce cours est une initiation à l’analyse de données. Il est préférable d’avoir une connaissance minimale de R. Dans le cas contraire, un tutoriel d’initiation est disponible sur la page web du cours et les notions de base de R seront rappelées pendant la pratique. Pour les personnes n’ayant jamais utilisé R, il peut être utile d’avoir des connaissances de base en programmation, quel que soit le langage.

Les cours seront donnés en Français et alterneront théorie et pratique avec RStudio. Il est demandé à chaque participant de venir avec un ordinateur portable chargé sur lequel il aura préalablement installé les éléments nécessaires (R, Rstudio et les fichiers de données sur lesquels nous travaillerons). La liste complète des fichiers et logiciels nécessaires sera disponible sur la page web du cours une dizaine de jours avant le début de la session.

derniere session: Mar 2016

 

Access conditions

ouvert à tous, sur inscription.

No website documented
Trainees:
12 trainees / year
Training time:
10 day(s) / year
No upcoming session scheduled

LeiSHield training course on Next Generation Sequencing

Description

The primary aim of this course was to provide a basic understanding of the Leishmania genome, NGS technology and analysis tools, and to develop a basic pipeline for the students to start working on their data. This first pipeline will help to standardize all analysis done in the consortium and should facilitate a posterior paper publication. This pipeline will evolve
in the context of a collaboration between the Leishield partners and the C3BI, taking into account the difficulties to analyze and interpret the sequence data generated, and the specific needs of each Consortium node. A future Workshop will be organized in June 2016 to tackle all these questions, and to have a follow-up on the analysis.

Access conditions

belonging to the Leishield consortium.

No website documented
Trainees:
20 trainees / year
Training time:
11 day(s) / year
No upcoming session scheduled

Programmation et scripting

Description

 Ce cours s'adresse à toute personne de l'institut Pasteur ou appartenant au réseau international (RIIP) souhaitant acquérir des bases de la programmation et du scripting utiles à la bioinformatique et ayant du mal à trouver du temps pour se former tout le long de l'année.

  • Initiation unix 3 jours
  • Programmation Python 6 jours
  • Utilisation d'un cluster de calcul 1 jour
  • Biopython 2 jours

 

Access conditions

Membre de l'institut Pasteur ou au réseau international de l'Institut  Pasteur (RIIP)

Formation universitaire

Trainees:
20 trainees / year
Training time:
30 day(s) / year
Upcoming session :
01-11-2017

Cours Pasteur Analyse des Génomes

Description

Chaque année, ce cours théorique et pratique d’une durée de sept semaines fait le tour
des concepts, techniques et outils nécessaires à l'étude des génomes, des étapes expérimentales à l’analyse des résultats. Il illustre les différents aspects de la génomique et de ses applications en se basant sur les résultats les plus récents de la recherche - voir plus

Access conditions
Not documented
Trainees:
15 trainees / year
Training time:
10 day(s) / year
Upcoming session :
13-02-2017

Rôles multiples de l’ARN

Description

Ce cours théorique et pratique de deux semaines est orienté sur les méthodes pour étudier la synthèse, maturation et la dégradation d’une large variété de molécules d’ARN dans les cellules eucaryotes - voir plus

Access conditions
Les candidats doivent avoir de bonnes connaissances en génétique, biologie moléculaire et biochimie du niveau de la fin de première année de Master, ainsi qu’un niveau minimum (B1) en français ET en anglais. Les candidatures sont sélectionnées et évaluées par le Comité du cours.
Users distribution
International
77 %
National
19 %
Regional
0 %
Local
4%
Explanation about this distribution:

This statistics are based on the provenance of Mobyle Jobs

Platform's own projects

Not Documented

Collaborations
National projets
Not documented
International and European projects
ELIXIR-EXCELERATE:
  • Work Package 1: "Tools Interoperability and Service Registry".
  • Work Package 4: "Compute, Data access and exchange services"
Projects with industry
Not documented
Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

In 2016

Seminars

The C3BI organize almost every thursday afternoon seminars on a wide range of bioinformatic subjects.
These seminars are free but upno registration for non pasteurians people.

Hackathons

Resource Hackathon : de.NBI EDAM Codefest (Jan 19-20 2016, Freiburg Uni., DE)
http://tinyurl.com/registryhackathon7
This hackathon, organised by University of Freiburg, will focus on 1) annotation of de.NBI tools and services, 2) ELIXIR Registry and registration process and 3) Publishing tools in the ELIXIR Registry.

Resource Hackathon : bio.tools @ Debian Med Sprint (Feb 4-7 2016, Lyngby, DK)
https://wiki.debian.org/Sprints/2016/DebianMed2016
Co-located with the Debian Med sprint: a resource hackathon focussed on curation and software development towards annotation and registration of tool packages from Debian Med.

Resource Hackathon : French Tools & Data Services (Mar 24-25, 2016, IFB, Gif-sur-Yvette, FR)
http://tinyurl.com/registryhackathon6
A hackathon bringing together representatives of French bioinformatics communities with the ELIXIR Tools & Data Services Registry, dedicated to the description and cataloguing of French tools and services, to boost their discovery and utility.
Technical Hackathon : Tools, Workflows and Workbenches (May 18-20, 2016, Institut Pasteur, Paris, FR)
http://tinyurl.com/registryhackathon8
A hackathon bringing together developers from key technical projects from ELIXIR and beyond including: the ELIXIR Tools & Data Services Registry (bio.tools), workbench/workflow projects (CWL, Galaxy, Taverna, Arvados), bioinformatics container solutions and registries, and the EDAM ontology.
Snakemake day FR, 2016
https://c3bi.pasteur.fr/news-journee-snakemake/
The day was a great opportunity for about 50 participants to learn about Snakemake, have high-level discussions about the syntax and usage, and to participate to some focus groups.
 

Schools

IFB G4B: Formation aux bonnes pratiques d'intégration d'outils sous Galaxy (29-02-2016 au 3-03-2016 Gif-sur-Yvette)
https://www.france-bioinformatique.fr/fr/cloud/formation-FG
AVISEAN-IFB: Initiation au traitement des données de génomique obtenues par séquençage à haut débit (20-11-2016 Roscoff)
http://www.france-bioinformatique.fr/fr/evenements/EBA2016

 

In 2015

Technical Hackathon 2 : EDAM development heuristics (Dec 1-4 2015, Amsterdam, Netherlands)

tinyurl.com/registryhackathon5

This hackathon aimed at preparing EDAM for scaling with registry growth.  The focus was to enumerate EDAM development heuristics to ensure usability, identify desirable clean-ups, and to devise quality assurance methods, including usability benchmarking in different scenarios.  It also included a thematic session focussing on protein structural biology and the WHAT-IF package.

Curation Hackathon 2 (Nov 4-6 2015, Brno, Czech Republic)

tinyurl.com/registryhackathon3

The second in the series, will aim for representation in the registry of all ELIXIR nodes, including new partners from Spain, Netherlands, Sweden and Finland, and other key resources beyond ELIXIR.

Thematic Hackathon 2 : RNA analysis (Sep 23-25 2015, Copenhagen, DK).  

A thematic hackathon focussed on RNA analysis and seeking to establish an ELIXIR RNA Tools Consortium that the Registry can draw upon in the future.

Thematic Hackathon 1 : defining good practice for resource annotation and registry curation (Aug 2015 23-25, Tallin, EE).

tinyurl.com/registryhackathon4

A three day workshop organised and financed by ELIXIR-EE aiming to identify relevant processes and good practice for the annotation and curation of resources for their integration into the emerging ELIXIR infrastructure, focussed on next generation sequencing (NGS) analysis and the SeqWIKI Resource Hub.

 

Technical Hackathon 1 - EDAM Development & Governance (Mar 2015, Lyngby, DK)

 

tinyurl.com/registryhackathon2

Focused on EDAM technical maintenance and usability, and produced a mock-up of tooling to assure optimal usage of EDAM for registry curation.

 

Participation to the G4B course

  • at La Chapelle-sur-Erdre  with the IFB-Galaxy working group (3 to 5 Mar. 2015)
  • at Toulouse with the IFB-Galaxy working group (2 to 5 Nov. 2015)

 

co-organizer and host of the hackathon and Galaxy Days, (Institut Pasteur, 18, 19 Nov. 2015)

Participation to the  France Génomique WP2.5 « Niveaux d'expression »

cea
cnrs
inra
inria
inserm
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