http://bioinfo.genotoul.fr/ [email protected] @BioinfoGenotoul Platform Genotoul Bioinfo Gaspin C., Hoede C., Klopp C., Laborie D., Mariette J., Noirot C., Trotard M.S. MIAT, Université de Toulouse, INRA, 31326 Castanet-Tolosan, France About us • Name: Platform Genotoul Bioinfo. • Creation year: 2000. • Location: INRA datacenter located in Auzeville, south of Toulouse. • Open to: the life science community requiring bioinformatics resources. • The team: 7 permanents (5.6 ETP). • Partnership: Genotoul Sequencing Patform (Get-Genotoul). • Network: • Genotoul facility (www.genotoul.fr). • French bioinformatics infrastructure (IFB « Institut Français de Bioinformatique »). • France genomic. Software and workflow developments The team develops novel data analysis methods and tools. The most recent tools include D-GENIES, an interactive dot plot viewer adapted to large genomes (Figure 1), and mixKernel,a R package to integrate heteroge- neous data (Figure 1). The team also sets up and maintains data analysis workflows. In 2017, three articles were published in collaboration with the Sigenae and SaAB teams. Figure 1: D-GENIES software output Figure 2: Integrating heterogenous data with mixKernel Training • In collaboration with: Sigenae, NED (GenPhySE), SaAB (MIAT) and TWB. • Thematics: RNAseq assembly, RNAseq mapping and quatification, sRNAseq, variant analysis, metagenomics. • Environment: Galaxy or command line. Data analysis Team members provide supports to biologists to analyse their data in various thematics: • genome assembly (short and long reads), • annotation (coding and non coding), • sRNA-seq, • RNA-seq, • methyl-seq, • variant analyses, • metagenomic (metabarcoding and whole genome), • and more recently data integration. In 2017, the platform was involved in 26 projects and has co-signed 17 publications with biologists. Figure 3: Part of the network representing predicted coevolution between L. monocytogenes EGD-e sRNAs and either 5’UTRs or CDS regions Computational resources • 3000 cores and a storage capacity of 2.5 Po. • Secure access (ssh) is provided to users ( 1200 users at the end of 2017). • Redundant equipments and daily back-ups also insure data protection and security. • More than 230 databanks are regularly updated. • 900 bioinformatic software were installed by the end of 2017. • VM hosting such as Galaxy instance maintained by the Sigenae team (http://www.sigenae.org/).

Gaspin C., Hoede C., Klopp C., Laborie D., Mariette J ...... [email protected] @BioinfoGenotoul Platform Genotoul Bioinfo Gaspin C., Hoede C., Klopp C., Laborie

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http://bioinfo.genotoul.fr/[email protected]@BioinfoGenotoul

Platform Genotoul Bioinfo

Gaspin C., Hoede C., Klopp C., Laborie D., Mariette J., Noirot C., Trotard M.S.MIAT, Université de Toulouse, INRA, 31326 Castanet-Tolosan, France

About us• Name: Platform Genotoul Bioinfo.• Creation year: 2000.• Location: INRA datacenter located in Auzeville, south of Toulouse.• Open to: the life science community requiring bioinformatics resources.• The team: 7 permanents (5.6 ETP).• Partnership: Genotoul Sequencing Patform (Get-Genotoul).• Network:

• Genotoul facility (www.genotoul.fr).• French bioinformatics infrastructure (IFB « Institut Français de Bioinformatique »).• France genomic.

Software and workflow developmentsThe team develops novel data analysis methods and tools. The most recenttools include D-GENIES, an interactive dot plot viewer adapted to largegenomes (Figure 1), and mixKernel, a R package to integrate heteroge-neous data (Figure 1). The team also sets up and maintains data analysisworkflows. In 2017, three articles were published in collaboration with theSigenae and SaAB teams.

Figure 1: D-GENIES software output Figure 2: Integrating heterogenous data withmixKernel

Training• In collaboration with: Sigenae, NED (GenPhySE), SaAB (MIAT)

and TWB.• Thematics: RNAseq assembly, RNAseq mapping and quatification,

sRNAseq, variant analysis, metagenomics.• Environment: Galaxy or command line.

Data analysisTeam members provide supports to biologists to analyse their data in variousthematics:• genome assembly (short and long reads),• annotation (coding and non coding),• sRNA-seq,• RNA-seq,• methyl-seq,• variant analyses,• metagenomic (metabarcoding and whole genome),• and more recently data integration.In 2017, the platform was involved in 26 projects and has co-signed 17publications with biologists.

Figure 3: Part of the network representing predicted coevolution between L. monocytogenesEGD-e sRNAs and either 5’UTRs or CDS regions

Computational resources

• 3000 cores and a storagecapacity of 2.5 Po.

• Secure access (ssh) is providedto users ( 1200 users at the end of2017).

• Redundant equipments and dailyback-ups also insure dataprotection and security.

• More than 230 databanks areregularly updated.

• 900 bioinformatic softwarewere installed by the end of 2017.

• VM hosting such as Galaxyinstance maintained by theSigenae team(http://www.sigenae.org/).

www.genotoul.fr

http://www.sigenae.org/