Projects per year
Time-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.
|Number of pages||6|
|Journal||Journal of biological rhythms|
|Publication status||Published - Aug 2012|
- Systems Biology
- Circadian rhythms
- Biological Clocks
- mathematical modeling
FingerprintDive into the research topics of 'The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models'. Together they form a unique fingerprint.
- 3 Finished
A modelling portal for the UK plant systems biology community
Millar, A., Tindal, C., Muetzelfeldt, R. & Ougham, H.
16/09/08 → 15/09/10
Regulation of biological signalling by temperature (ROBUST)
Halliday, K., Gilmore, S. & Millar, A.
14/04/08 → 13/10/13
SynthSys; formerly CSBE: Centre for Systems Biology at Edinburgh
Millar, A., Beggs, J., Ghazal, P., Goryanin, I., Hillston, J., Plotkin, G., Tollervey, D., Walton, A. & Robertson, K.
8/01/07 → 31/12/12
Plant Systems Modelling database
Millar, A. (Creator), University of Edinburgh, 2009
https://fairdomhub.org/projects/129 and one more link, http://www.plasmo.ed.ac.uk (show fewer)