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.
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Acknowledgements
The development of Reactome is supported by a grant from the US National Institutes of Health (P41 HG003751), EU grant LSHG-CT-2005-518254 “ENFIN,” Ontario Research Fund, and the EBI Industry Programme.
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Croft, D. (2013). Building Models Using Reactome Pathways as Templates. In: Schneider, M. (eds) In Silico Systems Biology. Methods in Molecular Biology, vol 1021. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-450-0_14
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DOI: https://doi.org/10.1007/978-1-62703-450-0_14
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