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dc.contributor.authorAdams, RR
dc.contributor.authorTsorman, N
dc.contributor.authorStratford, K
dc.contributor.authorAkman, OE
dc.contributor.authorGilmore, S
dc.contributor.authorJuty, N
dc.contributor.authorLe Novère, N
dc.contributor.authorMillar, AJ
dc.contributor.authorMillar, AJ
dc.date.accessioned2017-03-09T15:25:40Z
dc.date.issued2012-08-01
dc.description.abstractTime-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.en_GB
dc.description.sponsorshipK.S. was supported by the UK BBSRC grant BB/E015263/1. SynthSys Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1.en_GB
dc.identifier.citationVol. 27 (4), pp. 328 - 332en_GB
dc.identifier.doi10.1177/0748730412451077
dc.identifier.urihttp://hdl.handle.net/10871/26405
dc.language.isoenen_GB
dc.publisherSAGE Publications for Society for Research on Biological Rhythmsen_GB
dc.relation.urlhttps://www.ncbi.nlm.nih.gov/pubmed/22855577en_GB
dc.rightsOpen access under a Creative Commons licence: https://creativecommons.org/licenses/by/2.5/en_GB
dc.subjectAlgorithmsen_GB
dc.subjectAnimalsen_GB
dc.subjectCircadian Clocksen_GB
dc.subjectCircadian Rhythmen_GB
dc.subjectComputational Biologyen_GB
dc.subjectModels, Biologicalen_GB
dc.subjectProgramming Languagesen_GB
dc.subjectReproducibility of Resultsen_GB
dc.subjectSoftwareen_GB
dc.titleThe Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock modelsen_GB
dc.typeArticleen_GB
dc.date.available2017-03-09T15:25:40Z
exeter.place-of-publicationUnited Statesen_GB
dc.descriptionLetteren_GB
dc.descriptionThis is the final version of the article. Available from SAGE Publications via the DOI in this record.en_GB
dc.identifier.journalJournal of Biological Rhythmsen_GB


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