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Compact Representation of Photosynthesis Dynamics by Rule-based Models

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BRIM Luboš NIŽNAN Juraj ŠAFRÁNEK David

Rok publikování 2015
Druh Článek ve sborníku
Konference 5th International Workshop on Static Analysis and Systems Biology (SASB 2014)
Fakulta / Pracoviště MU

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Citace
Doi http://dx.doi.org/10.1016/j.entcs.2015.06.008
Obor Informatika
Klíčová slova Biological models; model annotation; systems biology; simulation; database
Popis 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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