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Responsable de publication :
Olivier Martin

Responsable éditoriale :
Rozenn Le Guyader

Administrateur de l'infoservice :
Thierry Balliau

ABI -  SOFT group

Permanent staff

Yannick DE OLIVEIRA, IE INRA

Pierre MONTALENT, IE INRA

Delphine STEINBACH, IR INRA

Other members of the group ABI-SOFT

26/10/18

  • Laëtitia Courgey : (Septembre 2018- Septembre 2020) : Apprenticeship student : Master 1 MIAGE SI (Information System), University Paris Dauphine
  • Mélanie POLARD-DONAT (September 2018-...): CDD IE INRA, software engineer on ThaliaDB project (PIA Amaizing funding), in collaboration with GQMS team

Previous collaborators: see below

 

Missions

To develop and to maintain databases and analysis tools useful for scientists in the lab, to make available those tools outside unit to help the scientific community and theirs partners at national and international level (plant communities).

  • Alice Beaugrand (August 2016 – August 2018): CDD IE INRA, software engineer on ThaliaDB project (PIA Amaizing funding), in collaboration with GQMS team
  • 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
  • Mélanie Polart-Donat (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student on SHiNeMaS project, in collaboration with DEAP team
  • Eva Dechaux (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student, on SHiNeMaS project, in collaboration with DEAP team.

To maintain for scientists of the lab, an environment (tools and databanks) for data analysis, through the setting of a Galaxy server. Our activities consist in :

  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).

To train scientists (local and their partners) to use tools developped or maintained in ABI-SOFT.

ABI-SOFT group needs servers to perform its activities. It benefits from the support of the ABI-SYS group for the system administration of its 3 servers and for access to the office softwares.

 

Current projects

ABI-SOFT has today 5 main software development projects that are 5 components of an information system providing scientists a research environment for data management and data analysis.

1) ThaliaDBThaliaDB print screen

In collaboration with GQMS team

ThaliaDB, a Web application/database that manages plant accessions (populations, lines, hybrids), seedlots, SNP markers, genotyping (rawdata, imputed/non imputed/filtered) and field phenotyping (elaborate, adjusted) data.

This tool is a component of a proximity information system developed in ABI-SOFT group. It is useful for lab data management, data curation, to prepare datasets for diversity analysis, for GWAS or genomic selection analysis and for data sharing with partners and external data repositories. Its is developped following 'Findable, Accessible, Interoperable, Reusable' principles. Data are managed by scientists themselves. Development and support is done by ABI-SOFT. A new version (a V3 in Django/python), dedicated to highthrouput data started in 2015 and is now in production for maize data, taking into account the migration of data maintained in previous versions V1,V2 (JAVA). The tool is accessible on-liner. It  is used today to manage data produced by GQMS team and their partners in the frame of scientific projects, such as Amaizing (investment for the future project, coord. A. Charcosset INRA GQE - le Moulon, (2011-2019), or from european projects such as DROPS (DROught-tolerant yielding PlantS, Coord. F. Tardieu LEPSE). It contains today maize data from 53 projects and experiments : for example genotyping results from 50 000 (50K) SNP markers genotyping chip, 600K Affymetrix Axiom chip, or from Genotyping By Sequencing technology: 900K markers, Cornell University collaboration).  Another instance is deployed for tomato in GAFL INRA laboratory, and perspectives, through INRA SelGen metaprogram, are to test it for other species such as wheat, rapseed or trees. Access to users (public research, partners from private compagnies), is provided with a user account. The tool was presented as a Poster at the recent European Conference of Computational biology in Athens, 2018. A computer demo is planned at the next Plant and Animal international conference in San Diego, 2019. The source code is maintained on RENATER SourceSup repository. A paper is in preparation. Contact : Delphine.Steinbach AT inra.fr for more information and collaboration.

2) SHiNeMaSSHiNeMaS

In collaboration with DEAP team

SHiNeMaS (Seeds History Management and Network System), a web application and 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 Wheat genome, in a context of participative science, agroecology and biological agriculture. Other instances on other species are in development in collaboration with external partners such as the members of the RSP, the ‘Réseau des Semences paysannes’, the collaboration with RSP started in 2003.

A paper is in preparation: "SHiNeMaS : A database and its web interfaces dedicated to seed lots history, phenotyping and cultural practices" by Yannick De Oliveira, Laura Burlot, Isabelle Goldringer, Darkawi Madi, Pierre Rivière, Delphine Steinbach, Gaëlle van Frank and Mathieu Thomas.

2018: the first version of SHiNeMaS is available here.

 

 

Biomercator printscreen3) Biomercator

In collaboration with GQMS team

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. ArcadeA. LabourdetteM. FalqueB. ManginF. ChardonA. Charcosset, and J. Joets, in Bioinformatics 2004. The version 3 was published by O. SosnowskiA. Charcosset, and J. Joets in Bioinformatics 2012.
BioMercator (V4) is freely available from download. The new version currently in development (V5) will provide tools to do GWAS meta-analysis.

 

4) Moulaxy

In collaboration with teams of UMR

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.

Moulaxy print screen

5) 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 Cette adresse email est protégée contre les robots des spammeurs, vous devez activer Javascript pour la voir. , for more details and partnership.

 

Previous collaborators:

  • Alice Beaugrand (August 2016 – August 2018): CDD IE INRA, software engineer on ThaliaDB project (PIA Amaizing funding), in collaboration with GQMS team
  • Sulyvan Dollin (April - July 2018) : Master 1 GENIOMHE (GENomics Informatics and Mathematics for Health and Environment), University Paris-Saclay
  • Arthur Robieux (February  – July 2018): Master 2 AMI2B, University Paris-Saclay internship student on ThaliaDB project, in collaboration with GQMS team
  • 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
  • Mélanie Polart-Donat (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student on SHiNeMaS project, in collaboration with DEAP team
  • Eva Dechaux (February – July 2017): Master 2 AMI2B, University Paris-Saclay internship student, on SHiNeMaS project, in collaboration with DEAP team.
  • 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
  • Olivier Akmansoy (May – August 2016): Ecoles des Mines Douai internship student on ThaliaDB project (PIA Amaizing project funding), in collaboration with GQMS
  • Alice Beaugrand (March – August 2016): Master 2 AMIB Univ. Paris-Sud internship student on SHiNeMaS project, in collaboration with DEAP
  • Aichatou Aboubacar-Amadou (Avril – September 2016) : Master 2 Univ. Reims internship student on SHiNeMaS project, in collaboration with DEAP (ANR Wheatamix project)
  • 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
  • Guy Ross Assoumou (January 2012 – December 2015): CDD IE/Software engineer on ThaliaDB project (PIA Amaizing project funding), in collaboration with GQMS
  • Jocelyn Chêne (Mars – August 2015): Master2 Univ. Nantes internship student, database schema development for ANR Bakery project
  • 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
  • Marie Lefebvre (March 2014 – August 2014): Master2 Univ. Nantes internship student on SHiNeMaS project (SPEAL project funding) in collaboration with DEAP.

ABI Publications