Publication details

Compact Representation of Photosynthesis Dynamics by Rule-based Models

Authors

BRIM Luboš NIŽNAN Juraj ŠAFRÁNEK David

Year of publication 2015
Type Article in Proceedings
Conference 5th International Workshop on Static Analysis and Systems Biology (SASB 2014)
MU Faculty or unit

Faculty of Informatics

Citation
Doi http://dx.doi.org/10.1016/j.entcs.2015.06.008
Field Informatics
Keywords Biological models; model annotation; systems biology; simulation; database
Description Traditional mathematical models of photosynthesis are based on mass action kinetics of light reactions. This approach requires the modeller to enumerate all the possible state combinations of the modelled chemical species. This leads to combinatorial explosion in the number of reactions although the structure of the model could be expressed more compactly. We explore the use of rule-based modelling, in particular, a simplified variant of Kappa, to compactly capture and automatically reduce existing mathematical models of photosynthesis. Finally, the reduction procedure is implemented in BioNetGen language and demonstrated on several ODE models of photosynthesis processes.
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