Pathways and biological systems modelling group

GRaPe – Gene Reaction Protein Builder

Despite considerable advances in the topological analysis of metabolic networks, inadequate knowledge of enzyme kinetic rate laws and their associated parameter values still hampers large-scale kinetic modelling. Furthermore, the integration of gene expression and protein levels into kinetic models is not straightforward.

The GRaPe software was developed to enable the construction of kinetic models for large systems of metabolic reactions and associated gene expression processes. It generates generic rate equations for all reactions in a model and encompasses two robust methods for parameter estimation from time series of 'omics' data. It also allows for the seamless integration of gene expression and protein levels into a reaction and generates equations for both transcription and translation.

GRaPe figure



Adiamah DA, Schwartz JM (2012). Construction of a genome-scale kinetic model of Mycobacterium tuberculosis using generic rate equations. Metabolites 2: 382-97.
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Adiamah DA, Handl J, Schwartz JM (2010). Streamlining the construction of large-scale dynamic models using generic kinetic equations. Bioinformatics 26: 1324-31.
PubMed | Full text