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Bioinformatics platform

Introduction

The IBENS bioinformatics platform was created in 2014. It aims to provide bioinformatics analysis and scientific illustration services to research groups of the life science community.

Bioinformatics analyses are frequently downstream analyses of data produced by the IBENS genomics platform but can also involve data produced by other sequencing centers. These analyses fill in gaps for teams without bioinformatics resources. The platform also provides a scientific illustration service, for the development of high quality figures and illustrations for high impact journals or scientific communications.

Services

Data analysis
Scientific illustration
Bioinfo seminars
Computing cluster

Data analyses
The bioinformatics platform is specialized in NGS data analysis. The proposed services concern analyses that are commonly adopted by the community and for which tools were already developed. These analyses are:
- Sequencing data quality control
- Read files mapping on genome/transcriptome
- Gene expression quantification from read files
- Transcriptomics differential expression analysis
- Pathway enrichment from differential expression data

We also realize more advanced analyses like:
- Motif detection in sequence sets
- Differential exon usage
- ...

Moreover, the bioinformatics platform can also work on more exploratory projects thus with a lower reliability and guarantee on the results in agreement with the collaborator.

Scientific illustration
Clear and well presented results are of great importance for scientific communication. However, complex concepts can be difficult to describe on paper. The Scientific illustration service of the bioinformatics platform was created to help researchers achieve high quality figures for papers, grant proposals or presentations. Within the proposed services, we offer:
- Visual representation of data, from ideas, raw data or drafts
- Schematics of processes, as biological illustrations
- Creation of visual identity for laboratories, research teams, events etc.
- Custom tasks related to scientific graphic design

To achieve high quality results, we associate a deep knowledge of data analysis, design insights and creativity. Don’t hesitate to contact us if you have any sort of need related to scientific illustrations in general. For examples of previous illustrations, see our portfolio.

Bioinfo seminars
Every two Thursday, the platform organizes a bioinfo seminar in the IBENS. Here is the list of upcoming and past seminars.

Computing cluster: bioclust
Bioclust is the internal computing cluster of the IBENS, accessible to all MEMOLIFE LABEX members. It is managed by the bioinformatics platform. Currently, its capacity is 69 nodes for 1700 CPUs and 6Tb memory. Users execute jobs through the scheduler, Condor, to run tools from the large range o available software programs.

Collaborations

We are working with teams from different institutes (Collège de France, Hôpital St-Louis, ESPCI, etc.) and are open to discuss any data analysis project with members of any other institute.

Publications

ALFA: annotation landscape for aligned reads
M Bahin, B F Noel, V Murigneux, C Bernard, L Bastianelli, H Le Hir, A Lebreton, A Genovesio
2019, BMC Genomics, https://doi.org/10.1186/s12864-019-5624-2

RSAT 2018: regulatory sequence analysis tools 20th anniversary
N Thi Thuy Nguyen, B Contreras-Moreira, J A Castro-Mondragon, W Santana-Garcia, R Ossio, C D Robles-Espinoza, M Bahin, S Collombet, P Vincens, D Thieffry, J van Helden, A Medina-Rivera, M Thomas-Chollier
2018, Nucleic Acid Research, doi.org/10.1093/nar/gky317

Translation in astrocyte distal processes sets molecular heterogeneity at the gliovascular interface
AC Boulay, B Saubaméa, N Adam, S Chasseigneaux, N Mazaré, A Gilbert, M Bahin, L Bastianelli, C Blugeon, S Perrin, J Pouch, B Ducos, S Le Crom, A Genovesio, F Chrétien, X Declèves, JL Laplanche, M Cohen-Salmon
2017, Cell Discovery, doi: 10.1038/celldisc.2017.5