Salmonella Genome Scale Metabolic Reconstruction
The consensus Salmonella genome scale metabolic reconstruction as described by Thiele et al. in BMC Systems Biology 2011 and developed in part as a project under the Center for Systems Biology of EnteroPathogens is available as a zipped SBML (L2V1) XML file here. This file may be read by any software supporting the SBML format; however, for simulations it is necessary to use software capable of performing flux balance analysis. The Cobra ToolBox, as developed by the UCSD Systems Biology Group headed by Bernhard Palsson, provides a variety of functions for running simulations, including growth phenotypes, gene deletion studies, etc. The COBRA Toolbox has a number of other software dependencies, including MatLab as described at the openCOBRA SourceForge Repository.
Future efforts related to this project include building additional simulation power by including transcription and translation into the overall model and to constrain the simulations with multi-omics datasets. Please check back here periodically for applications, uses, and possible updates to this reconstruction.