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In Silico Systems Biology

Volume 1021 of the series Methods in Molecular Biology pp 273-283

Date:

Building Models Using Reactome Pathways as Templates

  • David CroftAffiliated withEMBL Outstation–European Bioinformatics Institute

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Abstract

The first steps of building a new model can be very time-consuming, involving consulting many research papers and then assembling a plausible network of reactions. In this chapter, tools for speeding up this process will be discussed. Reactome is a database containing extensive coverage of pathways in Homo sapiens and numerous reference species. It offers researchers wishing to create new models from scratch various tools for extracting the relevant reactions, complete with layout information. In this chapter, two use cases will be described, in which a modeller provides certain essential pieces of information and Reactome automatically constructs the basic models and then dumps them in SBML-ML format.

Key words

Reactome Pathway Reaction Model SBML Data