Bioinformatics

Objectives

We aim to develop appropriate bioinformatics tools for the management and harnessing of the next generation sequencing data and to make them available first to all partners of the ARCAD project and subsequently to an extended community. This will require the best new technologies to explore:

1. Complex high throughput sequence analysis ranging from assemblers, multialignment searches, SNP detection, phylogenetic analyses to reconstruct haplotypic blocks, synteny groups and metabolic pathways;
2. Several data models and databases to store heterogeneous data that will enable interoperability between systems;
3. Several Web interfaces to launch analyses, to synthesize, visualize, query and edit the results.

 We will:

• Set up a collaborative development environment to avoid redundancy and to facilitate future bioinformatics developments across organizations;
• Provide training in bioinformatics and support for bioinformatics projects hosted on the ARCAD platform;
• Collaborate (share software, workshop, mailing lists, and good practices) with other national as well as international bioinformatics platforms;
• Ensure quality control in bioinformatics research though a scientific user committee, documentation, data traceability and reliability, CECILL licences, indicator measurement.

Resources

The project will make use of the SouthGreen bioinformatics platform and computer facilities built around a 208 Nehalem cores computer cluster, a low latency Infiniband network, and a 16 To storage capacity.

Actions planned

WP1. Development of a collaborative bioinformatics network

Task 1.1 - Cataloguing existing software and resources belonging to participating institutions; integrating them and making them accessible via a single exploitation system.
Task 1.2 - Promoting the full integration of tools such as the interoperability of databases, homogenization of workflows with common modules, development of generic graphic and query interfaces on the Web.
Task 1.3 - Creation of a Web portal to access all regional bioinformatics resources.
Task 1.4 - Participation in meetings organized by the different ARCAD sub-projects.
Task 1.5 - Organization of training in bioinformatics.
Task 1.6 - Diffusion of information about the ARCAD project: Web portal, publications, international conferences.
Task 1.7 - Starting and/or maintaining collaborative projects with other national and international bioinformatics platforms (Bioinfo-GenoToul, URGI, CNG, GCP, GMOD).
Task 1.8 – Promoting a quality management system in compliance with the IBISA label and the ISO 9001 standard.

WP2. Module for data management

Task 2.1 - Data management: data collection, data storage and formatting.
Task 2.2 - Adaptation of existing databases: components of existing databases will be reused, Chado (genomics annotation), TropGene (markers, maps, phenotypes, QTL), GreenPhyl (phylogenomic information) and development of new components.
Task 2.3 - Controlled integration in database modules.
Task 2.4 - Integration of external data: i) Links between environments, phenotypes, genetic resources, and genotyping data (SNP), ii) Links between genotyping data (SNP), QTL, association values, and sequence genomics annotations
Task 2.5 - Development of Web interfaces based on user needs.
Task 2.6 - Regular interactions with the data providers: helpdesk, soliciting feedback, training, presentations of the ARCAD database.

WP3. Module for diversity analyses

Task 3.1 - Assembling 454 sequencing outputs, testing of methods and parameters.
Task 3.2 - SNP determination.Task 3.3 - Link to genotyping data (Illumina chips).
Task 3.4 - Haplotypes definition.Task 3.5 - Detection of intra-species selection.
Task 3.6 - Development of integrated convivial Web interfaces.
Task 3.7 - Regular interactions with the ARCAD scientific projects concerning diversity analyses.

WP4. Module for sequence annotation and orthologue gene prediction

Task 4.1 - Automatic sequence annotation using manually curated sources (e.g. UniProtKB/Swiss-Prot ), protein domains and others.
Task 4.2 - Improvement of existing tools (GOST) to allow high-throughput sequence analysis.
Task 4.3 - Prediction of paralogue and orthologue genes using phylogenetic methods.
Task 4.4 - Further development of Web interfaces for the visualization of analyses.
Task 4.5 - Detection of the inter-species selection.
Task 4.6 - Characterization of the evolutionary dynamics of orthologues (genetic divergence, codon usage, GC content, etc.), and availability of the descriptors through a database like OrthoMaM (Ranwez et al. 2007).
Task 4.7 - Interactions with ARCAD research teams concerned with comparative genomics (evolution and domestication, functional analyses).

Project team

Contract staff

Activity report Year 2010

Bioinformatics project activity report 2010