Abstract interpretation and application to logic programs
Journal of Logic Programming
Communicating and mobile systems: the &pgr;-calculus
Communicating and mobile systems: the &pgr;-calculus
Information Processing Letters
Communication and Concurrency
Dependency Analysis of Mobile Systems
ESOP '02 Proceedings of the 11th European Symposium on Programming Languages and Systems
A static analyzer for large safety-critical software
PLDI '03 Proceedings of the ACM SIGPLAN 2003 conference on Programming language design and implementation
Theoretical Computer Science - Special issue: Computational systems biology
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Simulation and verification for computational modelling of signalling pathways
Proceedings of the 38th conference on Winter simulation
Formal Molecular Biology Done in CCS-R
Electronic Notes in Theoretical Computer Science (ENTCS)
ESOP'03 Proceedings of the 12th European conference on Programming
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
Beta binders for biological interactions
CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
Graph theory for rule-based modeling of biochemical networks
Transactions on Computational Systems Biology VII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Systems biology, models, and concurrency
Proceedings of the 35th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Theoretical Computer Science
Rule-Based Modelling, Symmetries, Refinements
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
How liquid is biological signalling?
Theoretical Computer Science
A Process Model of Actin Polymerisation
Electronic Notes in Theoretical Computer Science (ENTCS)
Agile Modelling of Cellular Signalling (Invited Paper)
Electronic Notes in Theoretical Computer Science (ENTCS)
The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
Programming in Biomolecular Computation
Electronic Notes in Theoretical Computer Science (ENTCS)
Stochastic Semantics of Signaling as a Composition of Agent-view Automata
Electronic Notes in Theoretical Computer Science (ENTCS)
DNA'11 Proceedings of the 17th international conference on DNA computing and molecular programming
Computational biology: a programming perspective
Formal modeling
Probabilistic model checking of biological systems with uncertain kinetic rates
Theoretical Computer Science
Stochastic simulation of multiple process calculi for biology
Theoretical Computer Science
Containment in Rule-Based Models
Electronic Notes in Theoretical Computer Science (ENTCS)
Abstraction of graph-based models of bio-molecular reaction systems for efficient simulation
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
An analysis for proving probabilistic termination of biological systems
Theoretical Computer Science
Synthesis of biological models from mutation experiments
POPL '13 Proceedings of the 40th annual ACM SIGPLAN-SIGACT symposium on Principles of programming languages
Complex functional rates in rule-based languages for biochemistry
Transactions on Computational Systems Biology XIV
Complex Functional Rates in the Modeling of Nano Devices (Extended Abstract)
Electronic Notes in Theoretical Computer Science (ENTCS)
Enumeration approach to computing chemical equilibria
Theoretical Computer Science
Hi-index | 0.01 |
Cellular signalling pathways, where proteins can form complexes and undergo a large array of post translational modifications are highly combinatorial systems sending and receiving extracellular signals and triggering appropriate responses. Process-centric languages seem apt to their representation and simulation [1,2,3]. Rule-centric languages such as κ [4,5,6,7,8] and BNG [9,10] bring in additional ease of expression. We propose in this paper a method to enumerate a superset of the reachable complexes that a κ rule set can generate. This is done via the construction of a finite abstract interpretation. We find a simple criterion for this superset to be the exact set of reachable complexes, namely that the superset is closed under swap, an operation whereby pairs of edges of the same type can permute their ends. We also show that a simple syntactic restriction on rules is sufficient to ensure the generation of a swap-closed set of complexes. We conclude by showing that a substantial rule set (presented in Ref. [4]) modelling the EGF receptor pathway verifies that syntactic condition (up to suitable transformations), and therefore despite its apparent complexity has a rather simple set of reachables.