Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra

By Aviv Regev, William Silverman, Ehud Y. Shapiro. Pacific Symposium on Biocomputing, 2000

532 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Hardware and Architecture, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b4e4616b1bb7cea8335e0c3e3824d715b2009e11

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Citations in the corpus

The Space and Motion of Communicating Agents (2009, methodology): “Finally, inspired by pioneering work [72] on applying proce ss calculi to biology, a stochastic treatment of the behaviour of bigraphs is propo sed by Krivine, Milner and Troina [51], in the spirit of the stochastic κ-calculus by Danos et al [27]; it associates a stochastic rate to each reaction rul”
BioAmbients: an abstraction for biological compartments (2004, methodology): “In our previous work [19] we developed an abstraction for biomolecular systems using the π-calculus process algebra [13], and extended the calculus to accurately handle the quantitative aspects of biochemical systems [17].”
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review (2002, unknown): “To mention some omissions, no attention is paid to Petri nets (Goss and Peccoud, 1998; Hofestädt and Thelen, 1998; Matsuno et al ., DE JONG 2000; Reddy et al ., 1996), transformational grammars (Collado-Vides, 1989, 1996; Collado-Vides et al ., 1998), and process algebra (Regev et al ., 2001).”
Formal molecular biology (2004, result): “This is in line both with Regev’s direct representations of various biological pathways [23, 26], and with the second encoding provided in a preceding paper dealing with a multiset-based version of κ [7].”
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli (2005, unknown): “Most approaches start from discrete models, such as Petri nets [18], process algebras [19], concurrent transition systems [7], rewriting logic [13], and Boolean networks and their generalizations [6].”
Executable cell biology (2007, methodology): “Initial work along this line used a process calculus called pi-calculus 56 as a modeling language for molecular interactions 5 .”
Reversible Communicating Systems (2004, methodology): “Following Regev [4, 5], process algebras have been investigated recently for modeling biological systems.”
The Continuous pi-Calculus: A Process Algebra for Biochemical Modelling (2008, methodology): “The application of the π-calculus to biology is due to Regev and Shapiro [3], who identified the fundamental correspondence between cellular processes and concurrent computations [13].”
Rule-Based Modelling of Cellular Signalling (2007, unknown): “to propose Milner’s π-calculus [20], a minimal language for describing concurrent systems, as a language for modelling biological systems [21–23].”