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

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

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 can 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, post-structural 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.

Original languageEnglish (US)
Pages (from-to)270-280
Number of pages11
JournalMetabolic engineering
Volume14
Issue number3
DOIs
StatePublished - May 1 2012

Fingerprint

Metabolic engineering
Metabolic Engineering
Metabolic Flux Analysis
Protein Engineering
Workflow
Metabolic Networks and Pathways
Nucleic Acids
Software
Nucleic acids
Electric network analysis
Application programs
Visualization
Fluxes
Proteins
Engineers
Datasets

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology

Cite this

Copeland, W. B., Bartley, B. A., Chandran, D., Galdzicki, M., Kim, K. H., Sleight, S. C., ... Sauro, H. M. (2012). Computational tools for metabolic engineering. Metabolic engineering, 14(3), 270-280. https://doi.org/10.1016/j.ymben.2012.03.001
Copeland, Wilbert B. ; Bartley, Bryan A. ; Chandran, Deepak ; Galdzicki, Michal ; Kim, Kyung H. ; Sleight, Sean C. ; Maranas, Costas D. ; Sauro, Herbert M. / Computational tools for metabolic engineering. In: Metabolic engineering. 2012 ; Vol. 14, No. 3. pp. 270-280.
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Copeland, WB, Bartley, BA, Chandran, D, Galdzicki, M, Kim, KH, Sleight, SC, Maranas, CD & Sauro, HM 2012, 'Computational tools for metabolic engineering', Metabolic engineering, vol. 14, no. 3, pp. 270-280. https://doi.org/10.1016/j.ymben.2012.03.001

Computational tools for metabolic engineering. / Copeland, Wilbert B.; Bartley, Bryan A.; Chandran, Deepak; Galdzicki, Michal; Kim, Kyung H.; Sleight, Sean C.; Maranas, Costas D.; Sauro, Herbert M.

In: Metabolic engineering, Vol. 14, No. 3, 01.05.2012, p. 270-280.

Research output: Contribution to journalArticle

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Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight SC et al. Computational tools for metabolic engineering. Metabolic engineering. 2012 May 1;14(3):270-280. https://doi.org/10.1016/j.ymben.2012.03.001