Biologists use diagrams to represent complex systems of interaction between molecular species. These graphical notations encompass two types of information: interactions (e.g. protein complexation, modification, binding to a gene, etc.) and regulations (of an interaction or a transcription). Based on these structures, mathematical models can be developed by equipping such molecular interaction networks with kinetic expressions leading to quantitative models of mainly two kinds: ordinary differential equations for a continuous interpretation of the kinetics and continuous-time Markov chains for a stochastic interpretation of the kinetics. Since 2002, we investigate the transposition of programming concepts and tools to the analysis of living processes at the cellular level.
@InProceedings{fages:LIPIcs.ICLP.2010.2, author = {Fages, Fran\c{c}ois}, title = {{A Logical Paradigm for Systems Biology}}, booktitle = {Technical Communications of the 26th International Conference on Logic Programming}, pages = {2--3}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-939897-17-0}, ISSN = {1868-8969}, year = {2010}, volume = {7}, editor = {Hermenegildo, Manuel and Schaub, Torsten}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICLP.2010.2}, URN = {urn:nbn:de:0030-drops-25776}, doi = {10.4230/LIPIcs.ICLP.2010.2}, annote = {Keywords: temporal logic, model-checking, systems biology, hybrid systems} }
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