SimOptStrain specifications


Unique identifier OMICS_06463
Name SimOptStrain


This tool is not maintained anymore.

Publication for SimOptStrain

SimOptStrain citations


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] ue . Reduced number of genetic modifications also enables a faster and simpler experimental implementation. Alternately, one could directly aim for the minimal number of genes as the objective (e.g., SimOptStrain identifies the minimal number of genetic interventions). Likewise, if the host organism is predefined, then it is also possible to minimize the number of heterologous reactions that need […]


Computational Methods for Modification of Metabolic Networks

Comput Struct Biotechnol J
PMCID: 4477032
PMID: 26106462
DOI: 10.1016/j.csbj.2015.05.004

[…] s to maximize the theoretical maximum production, and then maximizes the biochemical production by the bilevel programming where the number of deleted reactions is limited . Different from OptStrain, SimOptStrain simultaneously adds and deletes reactions to maximize the biochemical production and the cellular growth in the outer and inner problems, respectively . Applying existing ideas for MRC an […]

SimOptStrain institution(s)
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA

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