Software tools for the metabolic modeling

The team devotes part of its efforts to the development of a software platform for the modeling of metabolic flux at the scale of the cell. The objective is to facilitate the reconstruction, exploitation and comparison of metabolic models, and to provide support for in silico experimentation, such as the prediction of metabolic function of one or more organisms under the influence of genetic and/or environmental perturbations, for example. The platform will enable the simultaneous manipulation of several models; for instance predictions for growth and metabolic flux between different candidate models for a given species, or exploration of metabolic differences between related bacteria. The first block of software developed, Cyclone, facilitates the requisition and exploitation of data which are present in the BioCyc [* Krummenacker M (2005)] metabolic databases.
 
 

In silico experiments with metabolism model
(click to enlarge)

 
  Bibliography
  [*] Krummenacker M, Paley S, Mueller L, Yan T, and Karp PD.
 “Querying and Computing with BioCyc Databases.”
 Bioinformatics. 2005. 21:3454-5.