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Genome-Scale Model Management and Comparison

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Systems Metabolic Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 985))

Abstract

Spurred by recent innovations in genome sequencing, the reconstruction of genome-scale models has increased in recent years. Genome-scale models are now available for a wide range of organisms, and models have been successfully applied to a number of research topics including metabolic engineering, genome annotation, biofuel production, and interpretation of omics data sets. The challenge is how to manage the large amount of data in genome-scale models and perform comparative analysis to gain new biological insights. In this chapter, important standards for genome-scale modeling are outlined. Furthermore, management strategies as well as existing repository and construction tools are discussed. As the comparison of models is an important aspect during the development and analysis stages, available methods are presented and existing software solutions are reviewed.

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Author information

Authors and Affiliations

  1. Division for Bioinformatics, Biocenter, Innsbruck Medical University, Innsbruck, Austria

    Stephan Pabinger & Zlatko Trajanoski

Authors
  1. Stephan Pabinger
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  2. Zlatko Trajanoski
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Corresponding author

Correspondence to Zlatko Trajanoski .

Editor information

Editors and Affiliations

  1. Cockrell School of Engineering, Dept. of Chemical Engineering, The University of Texas at Austin, E. Dean Keeton Street 200, Austin, 78712, Texas, USA

    Hal S. Alper

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Pabinger, S., Trajanoski, Z. (2013). Genome-Scale Model Management and Comparison. In: Alper, H. (eds) Systems Metabolic Engineering. Methods in Molecular Biology, vol 985. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-299-5_1

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  • DOI: https://doi.org/10.1007/978-1-62703-299-5_1

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-298-8

  • Online ISBN: 978-1-62703-299-5

  • eBook Packages: Springer Protocols

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