Projects

During the past 10 years the Bioinfo Genotoul platform team has build up a robust expertise in sequence analysis. This knowledge has been used in many software development as well as data analysis projects. This expertise can also contribute to the success of your project. Feel free to contact us using the project form.

Project name	Short description (click on the project name for full description)	Fundings	Period (coordinator)
BReIF	BReIF project aims to build an coherent e-infrastructure that supports FAIR and Open Sciences data managment and maintainable data portal.	PEPR "Agroécologie & Numérique"	2023 - 2028 (AF Adam-Blondon)
Symway	SymWay: A new symbiosis pathway for rhizobial infection and nodulation in legumes.	ANR	2022 - 2026 (JF Arrighi)
MuDiS4LS	Mutualized Digital Spaces for FAIR Life Sciences (MUDIS4LS)	PIA3 Equipex+	2021 - 2029 (Jacques van Helden)
OCCALDAT	OCCALDAT aims to develop the scientific and technological research center in computing and data of the COMUE UT, which will bring together the aspects of data, intensive computing and processing.	FEDER, Région	2021-2027
SecOccIn	Sequencing Occitanie Innovation (SeqOccIn)	FEDER, Région	2019-2022
HEV	Blood vessels and Cancer: molecular characterization of high endothelial venules (HEVs), specialized blood vessels which contribute to the fight against Cancer. Appel d’offre:Projets libres de recherche « Biologie et Sciences du Cancer »	INCA	2014-2016 (JP Girard)
MemRNase	RNase E is an essential enzyme that has a global role in RNA metabolism. It functions as part of a large macromolecular complex known as the RNA degradosome. The aim of the proposal is to explore the physiological role of the localization of RNase E to the inner cytoplasmic membrane.	ANR Blanc	2014-2016 (AJ Carpoussis)
Bioinfo-2012 Midi-Pyrénées	Ce projet vise à développer l’activité de la plate-forme de manière cohérente et complémentaire à l’existant pour augmenter la capacité de réactivité, faire face aux innovations nécessaires et rester à la pointe de l’offre d’accompagnement. Les évolutions visées sont ici la capacité d’hébergement et la mise en place de services spécialisés complémentaires à l’existant. Appel d’offre: Soutien à l’acquisition d’équipements structurants pour les plateformes mutualisées de recherche de Midi-Pyrénées.	FEDER, Région	2013-2014 (C. Gaspin)
Bio-Data-Cloud	The objective of the BIO DATA CLOUD project is to design and implement a cloud computing system adapted to the efficient production of high value-added data in the field of plant biotechnology.	AI Development of the Digital Economy – Cloud Computing – Big Data	2013–2015
IFB	The main goal of the Institut Français de Bioinformatique (IFB) is to provide core bioinformatics resources to the national and international life science research community in key fields such as genomics, proteomics, systems biology, etc.	ANR-IA Infrastructures	2012-2019 (JF Gibrat)
France Génomique	France Génomique aims to structure and strengthen France's capabilities and expertise in high-throughput sequencing, as well as the associated computing and analysis capabilities required.	ANR-IA Infrastructures	2011-2020 (P. Leber and D. Milan)
BACNET	BACNET aims to overcome the limitations of currently available bioinformatics tools for analyzing transcriptomics data in bacteria	ANR-IA Bioinformatics	2011-2016 (P.Cossart)
FUNHYMAT	FUNHYMAT project intends to increase knowledge in the assembly and functioning of microbial mats	ANR Blanc	2011-2014
Plateformes Génomique et Bioinformatique	Ce projet vise à acquérir et faire évoluer les équipement performants issus des nouvelles technologies afin d’accompagner au meilleur niveau les programmes de génomique et de bioinformatique.	CPER 2007-2013	2007-2013 (C. Gaspin et D. Milan)

BReIF

Innovation in agroecology relies on the ability to harness greater diversity in agricultural systems by drawing on knowledge of available resources and characterising them using various high-throughput approaches. In this context, integrating large amounts of heterogeneous data is recognised as a strategic challenge in order to make sense of it. The BReIF project aims to build a coherent e-infrastructure supporting data management in accordance with FAIR and Open Science principles and a maintainable data portal.

Symway

SymWay, for a new symbiosis pathway for rhizobial infection and nodulation in legumes is a project involving 3 partners: LSTM, LIPME and GenoToul- Bioinfo.

As a common feature, AeRLCK and AeCRK belong to families of genes coding for central players (RLCKs and CRKs) in plant signalling pathways, interacting with ligand-binding receptor-like kinases (RLKs) (Liang & Zhou, 2018; Lee et al., 2017). Therefore, based on rlck and crk early mutant phenotypes in A. evenia, and known RLCK and CRK functions, we hypothesize that AeRLCK and AeCRK interact with receptors and/or downstream signalling actors to mediate photosynthetic Bradyrhizobium perception, signal transduction and infection. The SymWay project has as main objective to address this hypothesis. For this, we intend:

1. to characterize the biological function of AeRLCK and AeCRK,
2. to identify their interacting proteins and roles in symbiosis, and
3. to investigate how these components have evolved to enable the Nod-independent symbiosis.

MuDiS4LS

The PIA3 project Mutualized Digital Spaces for FAIR Life Sciences (MUDIS4LS) brings together 39 teams from 14 organisations, 4 national data centres, 7 regional data centres and 6 national data-producing infrastructures. The budget allocated will fund the purchase of servers and high-speed storage, which will be shared between 22 IFB platforms, and will enable 13 people to be recruited.

MUDIS4LS is based on the skills and previous achievements of the IFB platforms: the National Network for Computing Resources (NNCR) and its pooled tasks forces, the active developments of the interoperability working group, the machine-readable data management plans (maDMP), and support for the life and health sciences communities in depositing their data in international open-access repositories. It also includes a strong training component to empower life scientists to manage, analyse and share their research data. The relevance of the project will be demonstrated through 5 case studies covering various fields of application and in which the problems of integrating and sharing multi-omics data are addressed:

1. combining imaging data with other omics data;
2. marine biology;
3. health (meeting the challenges of hosting health data);
4. microbial research;
5. agriculture.

Overall, MUDIS4LS will promote open science by providing life scientists with all the keys to making their data findable, accessible, interoperable and reusable (FAIR).

OCCALDAT

This project is coordinated by Université Fédérale Toulouse Midi Pyrénées. The partners are : Université Toulouse 1, Université Toulouse 2, Université Toulouse 3, Institut National Polytechnique de Toulouse, Institut National des Sciences Appliquées de Toulouse, École Supérieure de l’Aéronautique et de l’Espace, CNRS, INSERM, INRAE, Genotoul bioinfo facilities.

The objective of this project is the development of the scientific and technological research center in computing and data of the COMUE UT, which will bring together the aspects of data, intensive computing and processing.

OCCALDAT is committed to an infrastructure centered on data, the primary purpose of which is to break the functioning in silos characterizing the thematic processing chains to offer a space allowing cross-fertilization between disciplines. What is targeted is therefore the capitalization of academic data in a referencing and exchange space offering an environment in line with their FAIRisation. The operationalization of this data lake will be done via dedicated HPC and cloud services.

SecOccIn

EnglishFrançais

The INRA "Sequencing Occitanie Innovation" (SeqOccIn) project, jointly supported by Genotoul GeT and Bioinfo platforms, was selected as part of AP01 axis, "Stimulate innovation", of the Occitanie region call for projects entitled "Regional Platforms for Research and Innovation", from the Operational program ERDF-FSE MIDI-PYRENEES ET GARONNE 2014-2020.

Objective of the project:

The SeqOccIn project aims to acquire expertise on the contribution of long read sequencing to three applications:

• A1: Genome assembly and analysis of genome variations
• A2: Analysis of epigenetic marks
• A3: Metagenomes analysis (shotgun and metabarcoding)

Actions benefiting from a grant:

• Engineer recruitment for technological developments
• Data production and analysis
• Equipment

Total eligible cost: €6,000,000 including European Union: €4,800,000, Private partners: €769,650, Own funds: €430,350.

Le projet « Sequençage Occitanie Innovation » (soit SeqOccIn) de l’INRA, porté conjointement par les plateformes GeT et Bioinfo de Genotoul, a été sélectionné dans le cadre de l’axe AP01 « Stimuler l’innovation » de l’appel à projet « Plateformes Régionales de Recherche et d’Innovation » de la région Occitanie sur le programme Opérationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020.

Objectif du projet :

Le projet SeqOccIn a pour but d’acquérir de l’expertise sur l’apport du séquençage Long Read sur molécule unique dans les trois domaines d’étude suivants :

• Axe n° 1 : l’analyse des variations des génomes
• Axe n° 2 : l’analyse des marques épigénétiques
• Axe n° 3 : l’analyse des métagénomes

Actions bénéficiant d’une subvention :

• Embauche de personnel
• Développement, production et analyse de données
• Achat d’équipement

Coût total éligible : 6 000 000€ dont Union Européenne: 4 800 000€, Partenaires privés: 769 650€, Fonds propres: 430 350€.

Bio-Data-Cloud

The objective of the BIO DATA CLOUD project is to design and implement a cloud computing system adapted to the efficient production of high value-added data in the field of plant biotechnology. To achieve this, the project, which brings together the necessary expertise in bioinformatics and IT, will identify, integrate and then test, based on scenarios, all the building blocks needed to run, in cloud mode, processing chains for very large volumes of data, enabling the plant genetics and genomics sector to predict or otherwise determine the behaviour of the object of their study.

Institut Français de Bioinformatique (IFB)

The main goal of the IFB is to provide core bioinformatics resources to the national and international life science research community in key fields such as genomics, proteomics, systems biology, etc. To achieve this goal, the missions of the IFB infrastructure will be:

1. To provide support for biology programs, both in terms of project bolstering and users training;
2. To provide an IT infrastructure devoted to the management and analysis of biological data, in particular data generated by high-throughput technologies. This infrastructure will provide the required means to sustain the first mission. It will rely on sizeable hardware resources (High Performance Computation, large storage capacity) and will provide access to high-quality developments in terms of software tools and databases;
3. To encourage inventive and advanced technological developments between Life Science and Information Technology that address key research questions in ambitious scientific programs both at the national and European (ELIXIR initiative) levels

France Génomique

To face the challenge of structuring and reinforcing in France the high-throughput sequencing capabilities and know-how together with the necessary associated computing and analysis capacity, the steering committee of the «National infrastructures for biology and healthcare » call for proposals (one of the 2010 “Investissements d’Avenir” – Investments for the Future calls) has recognised the need to build an integrated and well-coordinated national infrastructure that will maintain and reinforce the French position in the international genomics landscape, and whose capacity and expertise will optimally meet the very high expectations of the French life sciences research community for genomic services. The CNS, the CNG, the regional sequencing platforms and the regional bioinformatics platforms (ReNaBi) are associated to the project. In that context, the GenoToul Bioinformatics platform, as a member of ReNaBi, will contribute more specifically to the bioinformatics developments on technology assessment and quality control, assembly software evaluation and regulation of gene expression.

BACNET

While the number of transcriptomic studies in bacteria has been rapidly growing, the development of bioinformatics tools to analyze these data has not kept pace. This project proposes to address the limitations of currently available bioinformatics tools for analyzing transcriptomics data through the following objectives:

1. We will improve upon the existing tools to integrate, compare and visualize various types of transcriptomics data from gene expression arrays, tiling arrays and deep sequencing studies.
2. We will develop programs to sytematically identify, analyze and compare unannotated small ORFs that may have physiologically important roles such as bacteriocins, toxin-anti-toxin systems, signaling and quorum sensing peptides or regulatory molecules.
3. We will develop novel network inference algorithms to identify and describe gene regulatory networks of ncRNAs and regulatory proteins, investigate their composition and dynamics and identify putative key targets. The study will focus on the food borne pathogen Listeria monocytogenes which has emerged as an outstanding model system in several areas in biology including transcriptomics.

FUNHYMAT

FUNHYMAT project intends to increase knowledge in the assembly and functioning of microbial mats. The mats that will be investigated are similar except for the level of petroleum contamination, which constitutes the forcing parameter affecting the mats. Microbial mats have been characterized growing on shore lines contaminated after oil spills. Although their biodegradation potential has already been highlighted, currently it is not understand how the complex network characteristic of the mat and its function is affected by the petroleum contamination. The assessment of pollution impact either at functional groups level or at community level is a real challenge to understand the overall response of microbial mats to pollution, therefore the specific assemblage and functioning of the microbial mats will be investigated at both levels.