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brianjamesschmidt / gim3e

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression (COBRApy)
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GIM3E for Python

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression

These modules were developed and written at the University of California, San Diego in the Systems Biology Research Group for the Systems Biology of EnteroPathogens project. This work was funded by the NIAID under interagency agreement Y1-AI-8401.

Please cite:

BJ Schmidt, A Ebrahim, TO Metz, JN Adkins, BØ Palsson, DR Hyduke. (2013) GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics.

Release history


Release       Date          Notes
1.0.3         11.12.2013    -Substantial GMS improvements, additional
                             updates are anticipated.
1.0.2         08.20.2013    -Change module structure to prepare for release.
                            -Note GMS is still a "development version" sampler
                             but runs stably and has been tested for E. coli core
1.0.1         08.17.2013    -Improved robustness of code
1.0.0         07.05.2013    -Initial release, submitted for publication