MOST: a software environment for constraint-based metabolic modeling and strain design

James J Kelley; Anatoliy Lane; Xiaowei Li; Brahmaji Mutthoju; Shay Maor; Dennis Egen; Desmond S Lun

doi:10.1093/bioinformatics/btu685

MOST: a software environment for constraint-based metabolic modeling and strain design

Bioinformatics. 2015 Feb 15;31(4):610-1. doi: 10.1093/bioinformatics/btu685. Epub 2014 Oct 17.

Authors

James J Kelley¹, Anatoliy Lane¹, Xiaowei Li¹, Brahmaji Mutthoju¹, Shay Maor¹, Dennis Egen¹, Desmond S Lun²

Affiliations

¹ Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ 08102, USA and Phenomics and Bioinformatics Research Centre and School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA 5095, Australia.
² Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ 08102, USA and Phenomics and Bioinformatics Research Centre and School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA 5095, Australia Center for Computational and Integrative Biology and Department of Computer Science, Rutgers University, Camden, NJ 08102, USA and Phenomics and Bioinformatics Research Centre and School of Mathematics and Statistics, University of South Australia, Mawson Lakes, SA 5095, Australia.

PMID: 25677126
DOI: 10.1093/bioinformatics/btu685

Abstract

Summary: MOST (metabolic optimization and simulation tool) is a software package that implements GDBB (genetic design through branch and bound) in an intuitive user-friendly interface with excel-like editing functionality, as well as implementing FBA (flux balance analysis), and supporting systems biology markup language and comma-separated values files. GDBB is currently the fastest algorithm for finding gene knockouts predicted by FBA to increase production of desired products, but GDBB has only been available on a command line interface, which is difficult to use for those without programming knowledge, until the release of MOST.

Availability and implementation: MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/.

Contact: dslun@rutgers.edu.

MeSH terms

Algorithms*
Animals
Computational Biology / methods*
Gene Knockout Techniques*
Metabolic Flux Analysis / methods*
Metabolic Networks and Pathways*
Models, Biological*
Software*