Mathematics Cell

Mathematics Cell of Toulouse Biotechnology Institute, Bio & Chemical Engineering, is focused on mathematical modeling of biochemical and microbial systems.

What Mathematics Cell proposes?

We work by project. A researcher or engineer of TBI of elsewhere can propose an idea of a joint project where MathsCell can bring:

  • our competence in mathematical modeling;
  • (co-)developing scientific software (R, Python, C++, …);
  • (co-)editing scientific papers with mathematical component based on our joint project.

How to create a joint project?

  1. After discussing about purpose and main ideas of a project candidate, MathsCell will do a short feasibility study of the project;
  2. If the project is estimated as feasible, MathsCell edits a project proposal where project steps, contribution of the parties and so on are defined;
  3. If our partner accepts it, the project can start.

Are there particular requirements/conditions for projects?

  • A project should enter in the scope of MathsCell scientific activities.
  • If a software will be developed, it should be distributed under OpenSource license.
  • If a paper is published based on our common project, MathsCell staff contributed to the project should be in co-authors.
  • Our partners are asked for a financial participation which will depend on project’s workload.

Past/current projects

  • IsoSolve, a project with MetaSys team of TBI. The goal was to propose a unified framework for NMR/MS measurements on isotopically labeled metabolites. Preprint.
  • Influx2020, a project with MetaToul/Metabolic network about adapting influx_si software to high throughput experimental context.
  • G3Mclass, a project with Dr. Marina Guvakova, researcher in the University of Pennsylvania. The goal of the project is to develop a classifier for fine exploring of metabolic markers.
  • MetaboHub2, we participate in Workpackage 3 Task 4 (flux modeling) of this national-wide french consortium.

Software developed

  • influx_si metabolic flux/concentration estimation based on isotopic measurements;
  • IsoSolve a unified framework for NMR/MS isotopic measurements;
  • Deriv symbolic differentiation of R code for mathematical expressions;
  • rmumps an R wrapper for MUMPS library for sparse linear system solving;
  • r2sundials an R wrapper for Sundials library for ODE/sensitivity problem solving.

Staff

  • Serguei Sokol, PhD in applied mathematics, IR INRAE.

Contact

email: Serguei.Sokol [at] insa-toulouse.fr

Mail:

INSA/TBI/Cellule Mathématiques
135, avenue de Rangueil
31077 Toulouse Cedex 04

Office: 417

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