Constraint-based EFMs computation with Answer Set Programming

aspefm is a hybrid computational tool based on Answer Set Programming (ASP) and Linear Programming (LP) that permits the computation of EFMs while implementing many different types of constraints.


Thermodynamic EFMs

tEFMs is a method for computing thermodynamically feasible elementary flux modes using equilibrium constants.



Matlab code to draw automatically every EFMs of a network in Celldesigner files with metatool


ACoM is a biclustering method based on the Agglomeration of Common Motifs for classifying elementary flux modes

Hybrid dynamic modelling of metabolic netwoks

Metabolism and cell cycle are two central processes in the life of a eukaryote cell. we propose to use a differential model of the central carbon metabolism extended into a hybrid system reproducing an imposed succession of the phases. This hybrid approach qualitatively provides a first step towards a better understanding of the crosstalks between cell cycle and metabolism.



Bioψ is a formalism to model biological processes from molecular details to networks. This computational approach, based on elementary bricks of actions, allows us to calculate on biological functions (e.g. process comparison, mapping structure–function relationships, etc.).



Sili2DGel is an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.).