| Method |
Description |
Reference |
Software |
File |
| OptORF |
Predicts gene deletions and overexpression to maximize product formation at the maximum growth rate.
|
Kim et al. BMC Systems Biol 2010
|
GAMS |
Download
|
| RELATCH |
Predicts the effects of gene deletions on metabolic fluxes.
|
Kim et al. Genome Biology 2012
|
GAMS |
Download
|
| SimOptStrain |
Predicts gene deletions and reaction additions to maximize product formation at the maximum growth rate.
|
Kim et al. PLOS One 2011
|
COBRA |
Download
|
| FOCAL |
Identifies conditions (media and gene deletions) so that a reaction of interest is essential for a measurable function (e.g. growth).
|
Tervo et al. Genome Biol 2012
|
GAMS |
Download
|
| BioMog |
Predicts a modified or de novo biomass equation that best agrees with mutant phenotypes.
|
Tervo et al. PLOS One 2013
|
GAMS |
Download
|
| CosMos |
Predicts reaction deletion, upregulation, or downregulation to maximize the minimum chemical production.
|
Cotten et al. Biotechnol J. 2013
|
GAMS |
Download
|
| BiMOMA |
Predicts gene deletions to maximize product formation at MOMA solutions.
|
Kim et al. PLOS One 2011
|
GAMS |
Download
|
