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Electronic Notes in Theoretical Computer Science (ENTCS)
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IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Graph Transformation for Topology Modelling
ICGT '08 Proceedings of the 4th international conference on Graph Transformations
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Theoretical Computer Science
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Modeling of Genetic Regulatory Network in Stochastic π-Calculus
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On algorithmic analysis of transcriptional regulation by LTL model checking
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A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems
IWANN '09 Proceedings of the 10th International Work-Conference on Artificial Neural Networks: Part II: Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living
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LPNMR '09 Proceedings of the 10th International Conference on Logic Programming and Nonmonotonic Reasoning
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From Biochemistry to Stochastic Processes
Electronic Notes in Theoretical Computer Science (ENTCS)
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Natural Computing: an international journal
Hybrid dynamics of stochastic programs
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On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Formal cell biology in biocham
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
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Proceedings of the 8th International Conference on Computational Methods in Systems Biology
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APCCM '09 Proceedings of the Sixth Asia-Pacific Conference on Conceptual Modeling - Volume 96
Robust satisfaction of temporal logic over real-valued signals
FORMATS'10 Proceedings of the 8th international conference on Formal modeling and analysis of timed systems
Process Algebra with Hooks for Models of Pattern Formation
Electronic Notes in Theoretical Computer Science (ENTCS)
Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration
Electronic Notes in Theoretical Computer Science (ENTCS)
Compartmental rule-based modeling of biochemical systems
Winter Simulation Conference
Communications of the ACM
On Parameter Synthesis by Parallel Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Simulating Signalling Pathways With BioWayS
Electronic Notes in Theoretical Computer Science (ENTCS)
An Algorithm for the Identification of Components in Biochemical Pathways
Electronic Notes in Theoretical Computer Science (ENTCS)
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Summary: BIOCHAM (the BIOCHemical Abstract Machine) is a software environment for modeling biochemical systems. It is based on two aspects: (1) the analysis and simulation of boolean, kinetic and stochastic models and (2) the formalization of biological properties in temporal logic. BIOCHAM provides tools and languages for describing protein networks with a simple and straightforward syntax, and for integrating biological properties into the model. It then becomes possible to analyze, query, verify and maintain the model with respect to those properties. For kinetic models, BIOCHAM can search for appropriate parameter values in order to reproduce a specific behavior observed in experiments and formalized in temporal logic. Coupled with other methods such as bifurcation diagrams, this search assists the modeler/biologist in the modeling process. Availability: BIOCHAM (v. 2.5) is a free software available for download, with example models, at http://contraintes.inria.fr/BIOCHAM/ Contact: Sylvain.Soliman@inria.fr