Algorithmic analysis of programs with well quasi-ordered domains
Information and Computation - Special issue: LICS 1996—Part 1
Rewriting logic: roadmap and bibliography
Theoretical Computer Science - Rewriting logic and its applications
Specification of real-time and hybrid systems in rewriting logic
Theoretical Computer Science - Rewriting logic and its applications
Computation: finite and infinite machines
Computation: finite and infinite machines
A model diagram layout extension for SBML
Bioinformatics
Petri net modelling of biological regulatory networks
Journal of Discrete Algorithms
Bioinformatics
Reachability in Petri Nets with Inhibitor Arcs
Electronic Notes in Theoretical Computer Science (ENTCS)
RTA'03 Proceedings of the 14th international conference on Rewriting techniques and applications
The maude LTL model checker and its implementation
SPIN'03 Proceedings of the 10th international conference on Model checking software
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems 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
Multiple representations of biological processes
Transactions on Computational Systems Biology VI
Backward trace slicing for rewriting logic theories
CADE'11 Proceedings of the 23rd international conference on Automated deduction
Backward trace slicing for conditional rewrite theories
LPAR'12 Proceedings of the 18th international conference on Logic for Programming, Artificial Intelligence, and Reasoning
Using conditional trace slicing for improving Maude programs
Science of Computer Programming
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This paper presents an extension of Pathway Logic, called Quantitative Pathway Logic (QPL), which allows one to reason about quantitative aspects of biological processes, such as element concentrations and reactions kinetics. Besides, it supports the modeling of inhibitors, that is, chemicals which may block a given reaction whenever their concentration exceeds a certain threshold. QPL models can be specified and directly simulated using rewriting logic or can be translated into Discrete Functional Petri Nets (DFPN) which are a subclass of Hybrid Functional Petri Nets in which only discrete transitions are allowed. Under some constraints over the anonymous variables appearing in the QPL models, the transformation between the two computational models is shown to preserve computations. By using the DFPN representation our models can be graphically visualized and simulated by means of well known tools (e.g. Cell Illustrator); moreover standard Petri net analyses (e.g. topological analysis, forward/backward reachability, etc .) may be performed on the net model. An executable framework for QPL and for the translation of QPL models into DFPNs has been implemented using the rewriting-based language Maude. We have tested this system on several examples.