Detailed Information on Publication Record
2015
Compact Representation of Photosynthesis Dynamics by Rule-based Models
BRIM, Luboš, Juraj NIŽNAN and David ŠAFRÁNEKBasic information
Original name
Compact Representation of Photosynthesis Dynamics by Rule-based Models
Authors
BRIM, Luboš (203 Czech Republic, belonging to the institution), Juraj NIŽNAN (703 Slovakia, belonging to the institution) and David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution)
Edition
316. vyd. Neuveden, 5th International Workshop on Static Analysis and Systems Biology (SASB 2014), p. 17-27, 11 pp. 2015
Publisher
Elsevier
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
Czech Republic
Confidentiality degree
není předmětem státního či obchodního tajemství
Publication form
electronic version available online
RIV identification code
RIV/00216224:14330/15:00083221
Organization unit
Faculty of Informatics
ISSN
UT WoS
000361966300003
Keywords in English
Biological models; model annotation; systems biology; simulation; database
Tags
International impact, Reviewed
Změněno: 6/5/2016 03:32, RNDr. Pavel Šmerk, Ph.D.
Abstract
V originále
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.
Links
| EE2.3.20.0256, research and development project |
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