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. https://www.mdpi.com/2227-9717/8/12/1649/s1

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Thermodynamic EFMs

tEFMs is a method for computing thermodynamically feasible elementary flux modes using equilibrium constants. https://figshare.com/articles/thermoEFM_zip/4620910

MPA





EFMdraw

Matlab code to draw automatically every EFMs of a network in Celldesigner files with metatool https://github.com/CcileMoul1/efmdraw





ACoM

ACoM is a biclustering method based on the Agglomeration of Common Motifs for classifying elementary flux modes http://savannah.nongnu.org/projects/acom-c

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. https://github.com/CcileMoul1/TheseMoulin



MPA





Bioψ

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.). https://www.sys2diag.cnrs.fr/index.php?page=biopsi-manager

MPA

Sili2Dgel

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.).
https://www.sys2diag.cnrs.fr/index.php?page=sili2dgel

MPA