Modelling the structure and dynamics of biological pathways

O’Hara, L. et al. (2016) Modelling the structure and dynamics of biological pathways. PLoS Biology, 14(8), e1002530. (doi: 10.1371/journal.pbio.1002530) (PMID:27509052) (PMCID:PMC4980033)

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Abstract

There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system’s dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems.

Item Type:Articles
Additional Information:TCF, MWB and PD are funded by an Institute Strategic Grant from the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/JO1446X/1]. Development of BioLayout Express3D was funded by BBSRC grants [BB/F003722/1, BB/I001107/1]. The development of the VirtuallyImmune.org website and model of influenza infection was funded by the NC3Rs “Crack it” challenge. TCF, LO, and LBS are funded by BBSRC grant [BB/J015105/1] to model pathways associated with Hypothalamic–Pituitary–Gonadal (HPG) axis, and LBS is supportedby an MRC grant [MR/N002970/1]
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Wright, Mr Derek
Authors: O’Hara, L., Livigni, A., Theo, T., Boyer, B., Angus, T., Wright, D., Chen, S.-H., Raza, S., Barnett, M. W., Digard, P., Smith, L. B., and Freeman, T. C.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:PLoS Biology
Publisher:Public Library of Science
ISSN:1545-7885
ISSN (Online):1545-7885
Copyright Holders:Copyright © 2016 O'Hara et al.
First Published:First published in PLoS Biology 14(8):e1002530
Publisher Policy:Reproduced under a Creative Commons License

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