Yeast 4.0 released!

{First posted 6 May 2010 at u003f.com, saved from oblivion by the internet archive}

One goal of integrative systems biology is the accurate representation of metabolite and protein interaction networks. To this end, several groups independently defined the metabolic network of baker’s yeast from available genomic and literature data [1,2]. These models differed considerably, so a “Jamboree” was held in Manchester in April 2007, bringing together experts from various disciplines to resolve discrepancies. The resultant reconstruction [3], known as Yeast 1.0, represents the first consensus, community-driven model of yeast metabolism.

A number of updates have made the model iteratively bigger and better since then. But Yeast 4.0 [4] represents a major advance in that it is the first to allow in silico experiments such as gene knockout analysis to be performed. Just install the COBRA toolbox, get the SBML model and, er, knock yourself out.

yeast mask from Planet Science

References

  1. Kuepfer L, Sauer U, & Blank LM (2005). Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome research, 15 (10), 1421-30 PMID: 16204195
  2. Mo ML, Palsson BO, & Herrgård MJ (2009). Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC systems biology, 3 PMID: 19321003
  3. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, & Kell DB (2008). A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature biotechnology, 26 (10), 1155-60 PMID: 18846089
  4. YeastNet: http://www.comp-sys-bio.org/yeastnet/
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