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@inproceedings{1301635,
author = {Brim, Luboš and Nižnan, Juraj and Šafránek, David},
address = {Neuveden},
booktitle = {5th International Workshop on Static Analysis and Systems Biology (SASB 2014)},
doi = {http://dx.doi.org/10.1016/j.entcs.2015.06.008},
edition = {316},
keywords = {Biological models; model annotation; systems biology; simulation; database},
howpublished = {elektronická verze "online"},
language = {eng},
location = {Neuveden},
pages = {17-27},
publisher = {Elsevier},
title = {Compact Representation of Photosynthesis Dynamics by Rule-based Models},
year = {2015}
}
TY - JOUR
ID - 1301635
AU - Brim, Luboš - Nižnan, Juraj - Šafránek, David
PY - 2015
TI - Compact Representation of Photosynthesis Dynamics by Rule-based Models
PB - Elsevier
CY - Neuveden
KW - Biological models
KW - model annotation
KW - systems biology
KW - simulation
KW - database
N2 - 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.
ER -
BRIM, Luboš, Juraj NIŽNAN and David ŠAFRÁNEK. Compact Representation of Photosynthesis Dynamics by Rule-based Models. Online. In \textit{5th International Workshop on Static Analysis and Systems Biology (SASB 2014)}. 316th ed. Neuveden: Elsevier, 2015, p.~17-27. ISSN~1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2015.06.008.
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