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Génétique Quantitative et Évolution - Le Moulon

ABI - SOFT group

Missions

ABI-Soft team aims to develop, deploy and provide analysis tools and databases useful for scientists of the lab. The team aims also to make them available to the plant science community through the French national forge for research and higher education (SourceSup) and efficient deployment solutions (virtual machines, containers).

ABI-Soft also provides a Galaxy environment to perform workflows developed in the lab. The team is in charge to deploy the tools on the server, design the workflow in Galaxy and if needed to develop new tools to embed the workflow. The team works in close collaboration with the ABI-SYS team to maintain the servers infrastructure hosting the tools of ABI-Soft team.

ABI-Soft is also in charge of the training of the scientists (local and their partners) to use the tools developed by ABI-SOFT.

Current projects

Currently, ABI-SOFT develops several data management and analysis tools that are components of a global information system dedicated to plant breeding.

ThaliaDB

In collaboration with GQMS team. ThaliaDB is a web application with its database that manages plant accessions, seeds lots, SNP markers, genotyping rawddata and field phenotyping elaborated data. This tool is useful for lab data management, for data curation, to prepare datasets for genome wide assocation studies or genomic selection analysis and for data sharing with partners and external data repositories (Dataverse).

ThaliaDB screen

ThaliaDB screen

The software development started in 2004, two versions were developped in JAVA langage. A new version (V3) in Python/Django framework/PostgreSQL/MongoDB started in 2015 for maize species and is now installed at QGE-Le Moulon. It is used to manage data produced by GQMS team and their partners in the frame of scientific projects, such as Amaizing at national, or at european projects (DROPS). Other instances will be deployed for other species and projects in the following months, in collaboration with external partners.

SHiNeMaS

SHiNeMaS screen

SHiNeMaS screen

In collaboration with DEAP team. SHiNeMaS (Seeds History Management and Network System) is a web application and its database (Python/Django/PostGreSQL) that manages relationships between seeds distributed in an network of farms and their field phenotypic evaluation results in several environments (climate, soil), (See figure left). The tool is used today for the management of data of several projects on bread wheat, in a context of participative science, agroecology and organic agriculture. Other instances on other species are in development in collaboration with external partners such as the members of the RSP (‘Réseau des Semences paysannes’), the collaboration with RSP started in 2003. SHiNeMaS is freely available, please visit the project page on SourceSup .

Biomercator

In collaboration with GQMS team.

Biomercator screen

Biomercator screen

Biomercator, an analysis tool (JAVA) useful for gene discovery involved in the variation of agronomical traits. It allows displaying genetic maps and genome annotation data (markers, QTLs). It provides tools for making meta-analysis of QTLS. The first version was published by A. Arcade, A. Labourdette, M. Falque, B. Mangin, F. Chardon, A. Charcosset, and J. Joets, in Bioinformatics 2004. The version 3 was published by O. Sosnowski, A. Charcosset, and J. Joets in Bioinformatics 2012.
BioMercator (V4) is freely available from the project page on SourceSup . The new version currently in development (V5) will provide tools to do GWAS meta-analysis.

Moulaxy

In collaboration with teams of GQE lab. Moulaxy, the local instance of Galaxy server, open to the lab, that gives access to specific softwares and workflows adapted to UMR user needs and expertise.

  1. installing tools and workflows according to user needs and their scientific projects
  2. to develop news tools focused to the scientific expertise of the lab (engineering of methods for example)
  3. to help to the valorization of those tools for example by promoting them in the Galaxy bioinformatics communities at national and international level (toolsheds deposits, training).

Please contact Yannick De Oliveira , for more details and partnership.

Previous staff

  • Alice Beaugrand (2016-2018), Master 2 University Paris-Saclay, then CDD (SHiNeMaS, ThaliaDB)
  • Artur Robieux (2018), Master 2 University Paris-Saclay (ThaliaDB)
  • Marine Daniel-Dit Andrieu (2017), Master 2 University Paris-Saclay (Phenofield-Validator)
  • Mélanie Polart-Donat (2017), Master 2 University Paris-Saclay (SHiNeMaS)
  • Eva Dechaux (2017), Master 2 University Paris-Saclay (SHiNeMaS)
  • Lan-Anh Nguyen (2016), DUT Université d’Auvergne, (ThaliaDB)
  • Olivier Akmansoy (2016), Ecoles des Mines Douai (ThaliaDB)
  • Aichatou Aboubacar-Amadou (2016), Master 2 Univ. Reims (SHiNeMaS)
  • Lydia Aït-Brahim (2014 – 2016), Master 2 Université Paris-Saclay, then CDD (Biomercator)
  • Guy Ross Assoumou (2012 – 2015), CDD IE/Software engineer (ThaliaDB)
  • Jocelyn Chêne (2015), Master 2 Univ. Nantes (ANR Bakery project)
  • Laura Burlot (2014), Master 2 Univ. Lyon, then CDD IE/ software engineer (SHiNeMaS)
  • Marie Lefebvre (2014), Master2 Univ. Nantes (SHiNeMaS)
  • Darkawi Madi (2012), Master 2 (SHiNeMaS)