Statecharts: A visual formalism for complex systems
Science of Computer Programming
Coloured Petri nets (2nd ed.): basic concepts, analysis methods and practical use: volume 1
Coloured Petri nets (2nd ed.): basic concepts, analysis methods and practical use: volume 1
Types and programming languages
Types and programming languages
Theoretical Computer Science - Natural computing
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Graphical rule-based representation of signal-transduction networks
Proceedings of the 2005 ACM symposium on Applied computing
Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
Electronic Notes in Theoretical Computer Science (ENTCS)
Modelling and simulation of biological processes in BlenX
ACM SIGMETRICS Performance Evaluation Review
A Language for Biochemical Systems
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Compositional Definitions of Minimal Flows in Petri Nets
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Bioinformatics
Rule-Based Modelling and Model Perturbation
Transactions on Computational Systems Biology XI
An automated translation from a narrative language for biological modelling into process algebra
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
The biochemical abstract machine BIOCHAM
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Transactions on Computational Systems Biology VII
A graphical representation for biological processes in the stochastic pi-calculus
Transactions on Computational Systems Biology VII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Coloured stochastic multilevel multiset rewriting
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
A Syntactic Abstraction for Rule-Based Languages with Binding
Electronic Notes in Theoretical Computer Science (ENTCS)
Bio-PEPAd: A non-Markovian extension of Bio-PEPA
Theoretical Computer Science
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
Foundational aspects of multiscale modeling of biological systems with process algebras
Theoretical Computer Science
Spatial modeling in cell biology at multiple levels
Proceedings of the Winter Simulation Conference
Hi-index | 0.00 |
This paper introduces a Language for Biochemical Systems (LBS) which combines rule-based approaches to modelling with modularity. It is based on the Calculus of Biochemical Systems (CBS) which affords modular descriptions of metabolic, signalling and regulatory networks in terms of reactions between modified complexes, occurring concurrently inside a hierarchy of compartments and with possible cross-compartment interactions and transport. Additional features of LBS, targeted towards practical and large-scale applications, include species expressions for manipulating large complexes in a concise manner, parameterised modules with a notion of subtyping for writing reusable modules, and nondeterminism for handling combinatorial explosion. These features are demonstrated through examples. A formal specification of LBS is then given through an abstract syntax and a general semantics which is parametric on a structure pertaining to the specific choice of target semantical objects. Examples of such structures for the specific cases of Petri nets, coloured Petri nets, ODEs and continuous time Markov chains are also given.