Protocol abstract

Nature Protocols 5, 93 - 121 (2010)
Published online: 7 January 2010 | doi:10.1038/nprot.2009.203

Subject Categories: Biochemistry and protein analysis | Computational and theoretical biology | Model organisms

A protocol for generating a high-quality genome-scale metabolic reconstruction

Ines Thiele1,2 & Bernhard Ø Palsson1

Network reconstructions are a common denominator in systems biology. Bottom–up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

  1. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
  2. Current address: Center for Systems Biology, Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.

Correspondence to: Bernhard Ø Palsson1 e-mail:


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