Model checking
Using Hybrid Concurrent Constraint Programming to Model Dynamic Biological Systems
ICLP '02 Proceedings of the 18th International Conference on Logic Programming
Lateral Inhibition through Delta-Notch Signaling: A Piecewise Affine Hybrid Model
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
Hybrid Modeling and Simulation of Biomolecular Networks
HSCC '01 Proceedings of the 4th International Workshop on Hybrid Systems: Computation and Control
NuSMV 2: An OpenSource Tool for Symbolic Model Checking
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
A Core Modeling Language for the Working Molecular Biologist (Abstract)
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Modelling, property verification and behavioural equivalence of lactose operon regulation
Computers in Biology and Medicine
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
A Language for Biochemical Systems
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
A Higher-Order Graph Calculus for Autonomic Computing
Graph Theory, Computational Intelligence and Thought
Dynamic Compartments in the Imperative Π-Calculus
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
A Port Graph Calculus for Autonomic Computing and Invariant Verification
Electronic Notes in Theoretical Computer Science (ENTCS)
A stochastic pi calculus for concurrent objects
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Biochemical reaction rules with constraints
ESOP'11/ETAPS'11 Proceedings of the 20th European conference on Programming languages and systems: part of the joint European conferences on theory and practice of software
Rule-based modeling of transcriptional attenuation at the tryptophan operon
Winter Simulation Conference
Modelling biological networks by action languages via answer set programming
ICLP'06 Proceedings of the 22nd international conference on Logic Programming
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Simulating bacterial transcription and translation in a stochastic π calculus
Transactions on Computational Systems Biology VI
CMBSlib: a library for comparing formalisms and models of biological systems
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Discrete event multi-level models for systems biology
Transactions on Computational Systems Biology I
From syntax to semantics in systems biology towards automated reasoning tools
Transactions on Computational Systems Biology IV
Adapting biochemical kripke structures for distributed model checking
Transactions on Computational Systems Biology VII
The attributed pi-calculus with priorities
Transactions on Computational Systems Biology XII
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Rule-Based modeling of transcriptional attenuation at the tryptophan operon
Transactions on Computational Systems Biology XII
A Probabilistic Model for Molecular Systems
Fundamenta Informaticae - Concurrency Specification and Programming (CS&P 2004)
Self-organized Patterning by Diffusible Factors: Roles of a Community Effect
Fundamenta Informaticae - Watching the Daisies Grow: from Biology to Biomathematics and Bioinformatics — Alan Turing Centenary Special Issue
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In this article we present the Biochemical Abstract Machine BIOCHAM and advocate its use as a formal modeling environment for networks biology. Biocham provides a precise semantics to biomolecular interaction maps. Based on this formal semantics, the Biocham system offers automated reasoning tools for querying the temporal properties of the system under all its possible behaviors. We present the main features of Biocham, provide details on a simple example of the MAPK signaling cascade and prove some results on the equivalence of models w.r.t. their temporal properties.