Stage Master 2 - Bioinformatique

 Stage · Stage M2  · 6 mois    Bac+5 / Master   Toulouse Biotechnology Institute · Toulouse (France)

 Date de prise de poste : 8 janvier 2024


Bio-informatique, Fluxomique, Isotopie


Scientific context & objectives:

MetaToul-Fluxomet is the metabolomic & fluxomic platform located in the TBI (Toulouse Biotechnology Institute) laboratory in Toulouse. In collaboration with the Mathematics Cell of TBI, MetaToul-FluxoMet develops and provides the scientific community with methodologies for the study of metabolism. One of these, 13C fluxomics aims at measuring the actual rates of biochemical reactions in the cells 1. This approach makes it possible to obtain qualitative and quantitative information on the metabolic pathways used by the cell by analyzing the incorporation of a labeled tracer molecule into the metabolism and using a suite of bioinformatics tools to calculate intracellular fluxes from isotopic data.

13C-fluxomics approaches rely on robust experimental design to improve the number of fluxes that can be calculated from a set of isotopic data and the precision of flux values.  The quality of the experimental design step can be greatly improved by using bioinformatics tools that enable maximization of these parameters by optimizing the isotopic composition of the label input.

The objective of this internship will be to create a Python3 software that can handle the critical design step of 13C-fluxomics2. The delivered tool will leverage the influx_si 3 Python package to test a high number of labelling inputs to get the most precise set of intracellular fluxes, and different DevOps methods for continuous integration & deployment to ensure maintainability and flexibility in the coding and release process.

To do this, the trainee will carry out the following steps:

  • Design the software architecture in close collaboration with researchers from a broad variety of fields (bioinformatics, biology, analytical chemistry, etc)
  • Develop the software and maintain version control through the Git ecosystem
  • Design a continuous integration and deployment pipeline using tools such as tox, Github actions and more (discussions will be conducted with the trainee to find the most appropriate system for this)

Recommended training:

Master student in bioinformatics and computer science:

Expected skills:

Knowledge of Python 3 and object-oriented programming is mandatory.

Knowledge of or interest in metabolism, biochemistry and/or analytical chemistry would be a plus.

The recruited student will evolve in a platform environment and therefore team spirit, good interpersonal contact as well as a strong scientific and technical curiosity are more than welcome.


Procédure : Please, send us by email: • A cover letter explaining your interest in this internship (1-page max) • A CV (max. 2 pages)

Date limite : 27 octobre 2023


Serguei Sokol & Loïc Le Grégam

Offre publiée le 25 septembre 2023, affichage jusqu'au 27 octobre 2023