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Graph Rewriting and Strategies for Modeling Biochemical Networks

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SYNASC '07: Proceedings of the Ninth International Symposium on Symbolic and Numeric Algorithms for Scientific Computing

Pages 407 - 414

https://doi.org/10.1109/SYNASC.2007.44

Published: 26 September 2007 Publication History

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Abstract

In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules, and generation of biochemical networks based on the representation of molecular complexes as a particular type of multigraphs with ports called molecular graphs. The advantage of this approach is to obtain for free a rewriting calculus which allows defining at the same level transformation rules and strategies for modeling rule selection and application, in order to prototype network generation.

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Krivine J(2017)Systems biologyACM SIGLOG News10.1145/3129173.31291824:3(43-61)Online publication date: 28-Jul-2017
https://dl.acm.org/doi/10.1145/3129173.3129182
Thompson-Walsh CHayman JWinskel G(2012)Containment in Rule-Based ModelsElectronic Notes in Theoretical Computer Science (ENTCS)10.5555/2952789.2952848284:C(125-137)Online publication date: 20-Jun-2012
https://dl.acm.org/doi/10.5555/2952789.2952848
Damgaard THøjsgaard EKrivine J(2012)Formal Cellular MachineryElectronic Notes in Theoretical Computer Science (ENTCS)10.5555/2952789.2952847284:C(55-74)Online publication date: 20-Jun-2012
https://dl.acm.org/doi/10.5555/2952789.2952847

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Graph Rewriting and Strategies for Modeling Biochemical Networks

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SYNASC '07: Proceedings of the Ninth International Symposium on Symbolic and Numeric Algorithms for Scientific Computing

September 2007

513 pages

ISBN:0769530788

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IEEE Computer Society

United States

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Published: 26 September 2007

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Krivine J(2017)Systems biologyACM SIGLOG News10.1145/3129173.31291824:3(43-61)Online publication date: 28-Jul-2017
https://dl.acm.org/doi/10.1145/3129173.3129182
Thompson-Walsh CHayman JWinskel G(2012)Containment in Rule-Based ModelsElectronic Notes in Theoretical Computer Science (ENTCS)10.5555/2952789.2952848284:C(125-137)Online publication date: 20-Jun-2012
https://dl.acm.org/doi/10.5555/2952789.2952848
Damgaard THøjsgaard EKrivine J(2012)Formal Cellular MachineryElectronic Notes in Theoretical Computer Science (ENTCS)10.5555/2952789.2952847284:C(55-74)Online publication date: 20-Jun-2012
https://dl.acm.org/doi/10.5555/2952789.2952847

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Graph theory for rule-based modeling of biochemical networks

Rule-based modeling of biochemical networks: Research Articles

Computational Analysis of Biochemical Networks: Detecting Novel Drug Targets

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