A protocol for generating a high-quality genome-scale metabolic reconstruction.
TLDR
This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.Abstract:
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.read more
Citations
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What is flux balance analysis
TL;DR: This primer covers the theoretical basis of the approach, several practical examples and a software toolbox for performing the calculations.
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A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
Jeffrey D. Orth,Tom M Conrad,Jessica Na,Joshua A. Lerman,Hojung Nam,Adam M. Feist,Bernhard O. Palsson +6 more
TL;DR: The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000 and an update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites.
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A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
TL;DR: Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.
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TL;DR: The Model SEED is introduced, a web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic models and introduces techniques to automate nearly every step of this process, taking ∼48 h to reconstruct a metabolic model from an assembled genome sequence.
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