Computational tools for metabolic engineering

Wilbert B. Copeland, Bryan A. Bartley, Deepak Chandran, Michal Galdzicki, Kyung H. Kim, Sean C. Sleight, Costas D. Maranas, Herbert M. Sauro
2012 Metabolic Engineering  
A great variety of software applications are now employed in the metabolic engineering field. These applications have been created to support a wide range of experimental and analysis techniques. Computational tools are utilized throughout the metabolic engineering workflow to extract and interpret relevant information from large data sets, to present complex models in a more manageable form, and to propose efficient network design strategies. In this review, we present a number of tools that
more » ... n assist in modifying and understanding cellular metabolic networks. The review covers seven areas of relevance to metabolic engineers. These include metabolic reconstruction efforts, network visualization, nucleic acid and protein engineering, metabolic flux analysis, pathway prospecting, poststructural network analysis and culture optimization. The list of available tools is extensive and we can only highlight a small, representative portion of the tools from each area.
doi:10.1016/j.ymben.2012.03.001 pmid:22629572 pmcid:PMC3361690 fatcat:xqnmydnnejcupp2ujup45krwnm