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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).

comment: <> (### Phenofield-Validator In collaboration with GQMS team and external partners (LEPSE, Biogemma) in the frame of PIA Amaizing and DROPS european projects
Phenofield-Validator, a validation tool for field phenotyping trial raw data. The tool allows to check automatically phenotyping data according to a set of rules defined by users. It takes as input a table file with several sheets (the template is excel compliant) that contains the results of the field data phenotyping and provides after command line job (Talend software) execution, as output a csv file with data that are Validated and (if errors are detected) a second file that contains Errors to correct, with a description of the rule that was violated to help scientists to correct the data before running new quality control. Perspectives are to load the validated trial data in a database to provide users the possibility to query several datasets at a time, to draw graphics to make comparison between datasets according to environments and treatments.)

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

Previous staff

  • Laetitia Courgey (2018-2020), Master MIAGE Paris Dauphine University (SHiNeMaS, ThaliaDB)
  • 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)

comment: <> ( * August 2016 – August 2018: CDD IE INRA, software engineer on ThaliaDB project (PIA Amaizing funding), in collaboration with GQMS team) comment: <> ( * March 2016 – August 2016: Master 2 AMIB Univ. Paris-Sud internship student on SHiNeMaS project, in collaboration with DEAP team) comment: <> (* Artur Robieux (February – July 2018): Master 2 AMI2B, University Paris-Saclay internship student on ThaliaDB project, in collaboration with GQMS team) comment: <> (* Marine Daniel-Dit Andrieu (February – July 2017): Master2 Biologie computationnelle (AMI2B), University Paris-Saclay, Internship Student on PhenoValidator project (UMR funding), in collaboration with GQMS and Amaizing project partners) comment: <> (* Mélanie Polart-Donat (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student on SHiNeMaS project, in collaboration with DEAP team) comment: <> (* Eva Dechaux (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student, on SHiNeMaS project, in collaboration with DEAP team.) comment: <> (* Lan-Anh Nguyen (April – August 2016): DUT Génie biologique et bioinformatique Université d’Auvergne, internship student on ThaliaDB project (PIA Amaizing project funding), in collaboration with GQMS team) comment: <> (* Olivier Akmansoy (May – August 2016): Ecoles des Mines Douai internship student on ThaliaDB project (PIA Amaizing project funding), in collaboration with GQMS) comment: <> (* Aichatou Aboubacar-Amadou (Avril – September 2016) : Master 2 Univ. Reims internship student on SHiNeMaS project, in collaboration with DEAP (ANR Wheatamix project)) comment: <> (* Lydia Aït-Brahim (February 2014 – august 2014): Master 2 internship student, (November 2014 - June 2016) : CDD IE/software engineer, on Biomercator project (PIA Amaizing funding), in collaboration with GQMS) comment: <> (* Guy Ross Assoumou (January 2012 – December 2015): CDD IE/Software engineer on ThaliaDB project (PIA Amaizing project funding), in collaboration with GQMS) comment: <> (* Jocelyn Chêne (Mars – August 2015): Master2 Univ. Nantes internship student, database schema development for ANR Bakery project) comment: <> (* Laura Burlot (March 2014 – September 2014) : Master 2 Univ. Lyon internship student, (October 2014 – December 2014) : CDD IE/ software engineer, SHiNeMaS project (CASDAR ProABiodiv), in collaboration with DEAP) comment: <> (* Marie Lefebvre (March 2014 – August 2014): Master2 Univ. Nantes internship student on SHiNeMaS project (SPEAL project funding) in collaboration with DEAP.)