Research internship completed on the construction of a model of the gene regulation network in B. Subtilis

Céline Chevalier (1st year Master bioinformatics) completed in September a 3 months research internship on the construction of a Boolean network for the regulation of Bacilius Subtilis.

The objective was to build both the influence graph and the Boolean rules for the dynamics of the regulatory network of B. Subtilis, which also take into account the links with the metabolism.

The data come from a recent article gathering the knowledge of the state of the art ( The interactions are referenced in an excel file.


The student implemented in python a tool which interprets the data in the excel file to extract the influences (activations/inhibitions/unknown) between genes, and deduce some Boolean rules for the activations of the genes of the network.

Various analyses have been conducted on the resulting influence graph and Boolean network. In particular, it turns out that the network, as described in the database, contains very few feedback loop.

The model obtained at the end includes metabolites as input. Therefore,  it will allow to compute putative steady states with respect to different metabolic fluxes operating in different stages of the B. Subtilis cell cycle.

Publications of LifeForm


Internships in Spring/Summer of 2016

Several LifeForm-related  internships took place this spring and summer; let us start with the French side:

  • Clara Scherbaum worked at LSV on Computing Cut Sets for Petri Nets; she developped unfolding-based techniques for determining sets of conditions to block from being satisfied so that some given place in the Net remains unmarked; such cut sets allow to ensure health properties in biological networks.
  • Juraj Kolčák studied Efficient Analysis of Boolean Networks under Parameter Uncertainty  in his master’s thesis accepted at Masaryk University, Brno, Czech Republic; the research was carried out at LSV under the joint supervision of Stefan Haar and Loïc Paulevé, together with master’s advisor David Safranek at Brno.
  • Hugues Mandon successfully completed his master’s thesis on Algorithms for cellular reprogramming  with Loïc Paulevé and Stefan Haar at LRI; he is now continuing as a PhD student at LSV under Stefan Haar and Loïc Paulevé.
  • Céline CHEVALIER worked with Loïc Paulevé at LRI on a logical model for transcription regulation in Bacillus subtilis ; the results of her internship are presented here .

In Newcastle,

Welcome to the LifeForm project

LifeForm is an INRIA associated team started in 2016 centered around  the cooperation between