A consensus reconstruction of yeast metabolism

Latest version: Yeast consensus reconstructions are now made available at yeast.sf.net, this page is left here only for historical purposes

SBML file with compartments| SBML file without compartments

This page is a portal to the consensus network model, as published in the article Herrgård, Swainston et al. (2008) "A consensus yeast metabolic reconstruction obtained from a community approach to systems biology" Nature Biotechnol. 26, 1155-1160.


A number of reconstructions of the metabolic network of yeast based on genomic and literature data have been published. However, due to different approaches utilized in the reconstruction as well as different interpretations of the literature, the earlier reconstructions have significant number of differences. A community effort resulted in a consensus network model of yeast metabolism, combining results from previous models.

Jamboree meeting

The members of the yeast systems biology network recognised that a single consensus reconstruction of the yeast metabolic network was highly desirable. A jamboree meeting took place in April 2007 at the Manchester Centre for Integrative Systems Biology where several groups engaged in creating a consensus network of yeast. While reconciling the different reconstructions was a major focus, the team was also very interested in standardizing the naming of metabolites and following other standard annotation procedures (eg MIRIAM).

Metabolic reconstruction

The starting point for this consensus reconstruction were two freely available metabolic network reconstructions, iMM904 and iLL672 containing information from 904 and 672 yeast genes, respectively. Both were derived from the first genome-scale metabolic network reconstruction for yeast iFF708, but they followed different processes and their results were also significantly different.

This reconstruction is provided in the following formats:

The Systems Biology Markup Language (SBML) is a file format that encapsulates a network of biochemical reactions and is understood by a large number of software applications (see www.sbml.org). The current yeast metabolic reconstruction resulted in a large SBML file and some programs have trouble loading such a large network (we have succeeded using it with COPASI and Cytoscape).