{"id":354,"date":"2016-05-12T16:14:02","date_gmt":"2016-05-12T14:14:02","guid":{"rendered":"http:\/\/vm-bioinfo-wp.toulouse.inra.fr\/?page_id=354"},"modified":"2016-12-16T18:07:26","modified_gmt":"2016-12-16T17:07:26","slug":"expertise","status":"publish","type":"page","link":"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/","title":{"rendered":"Expertise"},"content":{"rendered":"

During the past 10 years the Bioinfo Genotoul platform team has build up a robust expertise in sequence analysis<\/strong>. This knowledge has been used in many software development<\/a> 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<\/a>.<\/p>\n

\n\n\n\n\t\n\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t\n\t
Project name<\/th>Description<\/th>Fundings<\/th>Period (coordinator)<\/th>\n<\/tr>\n<\/thead>\n
SecOccIn<\/td> \"\"<\/a>
\n
\nThe 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.
\n
\nObjective of the project:
\n
\nThe SeqOccIn project aims to acquire expertise on the contribution of long read sequencing to three applications:
\n A1: Genome assembly and analysis of genome variations
\n A2: Analysis of epigenetic marks
\n A3: Metagenomes analysis (shotgun and metabarcoding)
\n
\nActions benefiting from a grant:
\n
\n- Engineer recruitment for technological developments
\n- Data production and analysis
\n- Equipment
\n
\nTotal eligible cost: \u20ac6,000,000 including European Union: \u20ac4,800,000, Private partners: \u20ac769,650, Own funds: \u20ac430,350.
\n
\n---
\nLe projet \u00ab Sequen\u00e7age Occitanie Innovation \u00bb (soit SeqOccIn) de l\u2019INRA, port\u00e9 conjointement par les plateformes GeT et Bioinfo de Genotoul, a \u00e9t\u00e9 s\u00e9lectionn\u00e9 dans le cadre de l\u2019axe AP01 \u00ab Stimuler l\u2019innovation \u00bb de l\u2019appel \u00e0 projet \u00ab Plateformes R\u00e9gionales de Recherche et d\u2019Innovation \u00bb de la r\u00e9gion Occitanie sur le programme Op\u00e9rationnel FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020.
\n
\nObjectif du projet :
\n
\nLe projet SeqOccIn a pour but d\u2019acqu\u00e9rir de l\u2019expertise sur l\u2019apport du s\u00e9quen\u00e7age Long Read sur mol\u00e9cule unique dans les trois domaines d\u2019\u00e9tude suivants :
\n
\n Axe n\u00b0 1 : l\u2019analyse des variations des g\u00e9nomes
\n Axe n\u00b0 2 : l\u2019analyse des marques \u00e9pig\u00e9n\u00e9tiques
\n Axe n\u00b0 3 : l\u2019analyse des m\u00e9tag\u00e9nomes
\n
\nActions b\u00e9n\u00e9ficiant d\u2019une subvention :
\n
\n - Embauche de personnel
\n - D\u00e9veloppement, production et analyse de donn\u00e9es
\n - Achat d\u2019\u00e9quipement
\n
\nCo\u00fbt total \u00e9ligible : 6 000 000\u20ac dont Union Europ\u00e9enne: 4 800 000\u20ac, Partenaires priv\u00e9s: 769 650\u20ac, Fonds propres: 430 350\u20ac.
\n<\/td>		FEDER, R\u00e9gion<\/td>2019-2022<\/td>\n<\/tr>\n
HEV<\/td>Blood vessels and Cancer: molecular characterization of high endothelial venules (HEVs), specialized blood vessels which contribute to the fight against Cancer. Appel d\u2019offre:Projets libres de recherche \u00ab Biologie et Sciences du Cancer \u00bb<\/td>INCA<\/td>2014-2016 (JP Girard)<\/td>\n<\/tr>\n
MemRNase<\/td>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.<\/td>ANR Blanc<\/td>2014-2016 (AJ Carpoussis)<\/td>\n<\/tr>\n
Bioinfo-2012 Midi-Pyr\u00e9n\u00e9es<\/td>Ce projet vise \u00e0 d\u00e9velopper l\u2019activit\u00e9 de la plate-forme de mani\u00e8re coh\u00e9rente et compl\u00e9mentaire \u00e0 l\u2019existant pour augmenter la capacit\u00e9 de r\u00e9activit\u00e9, faire face aux innovations n\u00e9cessaires et rester \u00e0 la pointe de l\u2019offre d\u2019accompagnement. Les \u00e9volutions vis\u00e9es sont ici la capacit\u00e9 d\u2019h\u00e9bergement et la mise en place de services sp\u00e9cialis\u00e9s compl\u00e9mentaires \u00e0 l\u2019existant. Appel d\u2019offre: Soutien \u00e0 l\u2019acquisition d\u2019\u00e9quipements structurants pour les plateformes mutualis\u00e9es de recherche de Midi-Pyr\u00e9n\u00e9es.<\/td>FEDER, R\u00e9gion<\/td>2013-2014 (C. Gaspin)<\/td>\n<\/tr>\n
Bio-Data-Cloud<\/td>L\u2019objectif du projet BIO DATA CLOUD est de concevoir et de mettre en \u0153uvre un syst\u00e8me de type cloud computing adapt\u00e9 \u00e0 une production efficace de donn\u00e9es \u00e0 haute valeur ajout\u00e9e dans le domaine de la biotechnologie v\u00e9g\u00e9tale. Pour se faire, ce projet qui r\u00e9unit les comp\u00e9tences n\u00e9cessaires en bioinformatique et en informatique, va permettre d\u2019identifier, d\u2019int\u00e9grer puis tester, \u00e0 partir de sc\u00e9narii, l\u2019ensemble des briques n\u00e9cessaires \u00e0 l\u2019ex\u00e9cution, en mode Cloud, des chaines de traitement de tr\u00e8s grand volumes de donn\u00e9es permettant au secteur de la g\u00e9n\u00e9tique et de la g\u00e9nomique v\u00e9g\u00e9tale de pr\u00e9dire ou autre le comportement de l\u2019objet de leur \u00e9tude.<\/td>IA D\u00e9veloppement de l\u2019Economie Num\u00e9rique \u2013 Cloud Computing \u2013 Big Data<\/td>2013-2015<\/td>\n<\/tr>\n
Institut Fran\u00e7ais de Bioinformatique (IFB)<\/td>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:
\n1. To provide support for biology programs, both in terms of project bolstering and users training;
\n2. 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;
\n3. 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<\/td>		ANR-IA Infrastructures<\/td>2012-2019 (JF Gibrat)<\/td>\n<\/tr>\n
France G\u00e9nomique<\/td>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 \u00abNational infrastructures for biology and healthcare \u00bb call for proposals (one of the 2010 \u201cInvestissements d\u2019Avenir\u201d \u2013 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.<\/td>ANR-IA Infrastructures<\/td>2011-2020 (P. Leber and D. Milan)<\/td>\n<\/tr>\n
BACNET<\/td>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.<\/td>ANR-IA Bioinformatics<\/td>2011-2016 (P.Cossart)<\/td>\n<\/tr>\n
Funhymat<\/td>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.<\/td>ANR Blanc<\/td>2011-2014<\/td>\n<\/tr>\n
Plateformes G\u00e9nomique et Bioinformatique<\/td>Ce projet vise \u00e0 acqu\u00e9rir et faire \u00e9voluer les \u00e9quipement performants issus des nouvelles technologies afin d\u2019accompagner au meilleur niveau les programmes de g\u00e9nomique et de bioinformatique.<\/td>CPER 2007-2013<\/td>2007-2013 (C. Gaspin et D. Milan)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n","protected":false},"excerpt":{"rendered":"

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....<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":16,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"page-templates\/child-menu.php","meta":[],"yoast_head":"\nExpertise - genotoul-bioinfo-UPDATE<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/\",\"url\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/\",\"name\":\"Expertise - genotoul-bioinfo-UPDATE\",\"isPartOf\":{\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#website\"},\"datePublished\":\"2016-05-12T14:14:02+00:00\",\"dateModified\":\"2016-12-16T17:07:26+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/\"]}]},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/expertise\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"About us\",\"item\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/index.php\/about-us\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Expertise\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#website\",\"url\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/\",\"name\":\"genotoul-bioinfo-UPDATE\",\"description\":\"\",\"publisher\":{\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#organization\"},\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"},{\"@type\":\"Organization\",\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#organization\",\"name\":\"genotoul-bioinfo-UPDATE\",\"url\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/\",\"logo\":{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#\/schema\/logo\/image\/\",\"url\":\"\",\"contentUrl\":\"\",\"caption\":\"genotoul-bioinfo-UPDATE\"},\"image\":{\"@id\":\"https:\/\/vm-bioinfo-wp.toulouse.inrae.fr\/genotoul_test_update\/#\/schema\/logo\/image\/\"}}]}<\/script>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Expertise - 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