Missions

The Biocomputing Hub goal is to lead and promote bioinformatics in the LBMC. The center actions are organized around 3 axes:

1. the development of standards for the laboratory

The Biocomputing Hub provides guides and toolboxes to facilitate collaboration between members of the laboratory.

For example, the Hub Biocomputing established:

• a guide of good practices to standardize the format of the projects.
• a data management guide to back up and share more easily the data generated in the laboratory
• a Gitlab server to share codes and scripts

2. the training

To make these tools accessible to all members of the laboratory and promote the sharing of methods, the Biocomputing Hub organizes training.

• Unix and command line
• R the basics
• Git the basics
• Nextflow

These training courses are often given in collaboration with the other laboratories of SFR-Bioscience and its Conseil d’Analyse Numérique (CAN).

3. Increasing the number projects between biologists and bioinformaticians

Benefiting from the axes 1 and 2, the members of the Biocomputing Hub are also involved in projects supported by members of the laboratory.

These projects are of three types:

• Support to biologists in the processing and analysis of their data
• Co-supervision of bioinformatics students
• Emergency interventions for deadlines related to publications

Projects

2021 Bernard team: Developpment of a normalization method for calibrated Chip-Seq data

To be able to analyze global variations of condesine occupancy on the whole genome of S. pombe we have developed a nextflow pipeline implementing the normalization proposed by Hu et al. We improved this normalization by proposing a calibrated normalization using the input data. This improvement allowed us to take into account the variations of chromatin accessibility in the observed signal as well as to be able to look at the condensin occupation at the repeated regions of the genome.

2019 ECBN team: Genome analysis of Mesorhabditis belari:

To better understand the mechanisms behind the reproductive strategy of the worm Mesorhabditis belari, which produces 9% of males, we have produced a hybrid assembly of its genome from WGS paired-end sequence (100 bp) at 200x as well as from long read at 10x (nanopore). The annotation of this genome was made using RNA-Seq data for the genes and DNA-Seq data for the repeated elements. We then used this assembly to identify sex-specific regions of the genome, as well as sex-specific SNPs. These SNPs and regions could then be used to design PCR probes or perform DNA FISH experiments.

2017 PRIO team: Automatic analysis of FACS data

Writing of an R package for the analysis of the stability of the TAL1 protein, involved in the development of acute T cell leukemia. This study was carried out by establishing T lymphocyte lines (Jurkat) expressing two fluorescent proteins: GFP and RFP fused to our protein, from the same mRNA (use of “self-cleaving sequences”). The RFP to GFP fluorescence ratio is used to assess the stability of the protein fused to RFP. The R package to be developed allows you to directly analyze FACS output files, and to perform automatic gating steps before analyzing data from dozens of different proteins for thousands of cells with a linear model.

You can consult the list of projects on which the members of the Hub Biocomputing intervene.

Internships

You can consult the list of internship subjects co-supervised or supervised by the Hub Biocomputing

Composition

The Biocomputing Hub is composed of 5 permanent members under the direction of Daniel Jost, Franck Mortreux and Laurent Modolo:

• Ghislain DURIF, IR CNRS (100%)

• David CLUET, IR CNRS (20%)

• Nicolas Fontrodona, IE, ENS (30%)

• Stéphane JANCZARSKI, IE CNRS (20%)

• Stève de BOSSOREILLE, IR CNRS (20%)

The Hub members are in charge of the executing the missions of the Biocomputing Hub such as training and the implementation of standards as well as accompanying or co-supervising projects, hold by LBMC members’.

Biocomputing Committee

The Biocomputing Committee is made up of 15 members, meeting several times a year to decide on the future actions of the Hub Biocomputing.

During these meetings, the Committee will:

• Create surveys to identify the needs of the members of the laboratory
• Plan training courses
• Create animations around bioinformatics

The minutes of the meetings of the Committee are available online

Steering Committee

A Steering Committee, made up of team leaders, is responsible for evaluating and awarding projects supported by members of the laboratory.

These projects are then attributed to the members of the Hub Biocomputing.

The list of these projects is available online

Biocomputing Hub Publications