On parameter synthesis by parallel model checking

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 3, 2012, Pages 693-705

  Barnat, Jiří ^a   Brim, Luboš ^a   Krejčí, Adam ^a   Streck, Adam ^a   Šafránek, David ^a   Vejnar, Martin ^a   Vejpustek, Tomáš ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Biological networks; dynamical systems; parallel model checking; parameter synthesis; systems biology.

Indexed keywords

BIOLOGICAL MODELS; BIOLOGICAL NETWORKS; COMPUTATIONAL SYSTEMS BIOLOGY; MODELING APPROACH; NOVEL ALGORITHM; PARALLEL MODEL CHECKING; PARAMETER SYNTHESIS; PARAMETER UNCERTAINTY; SYSTEMS BIOLOGY.;

ALGORITHMS; DYNAMICAL SYSTEMS; MODEL CHECKING; UNCERTAINTY ANALYSIS;

BIOLOGICAL SYSTEMS;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; METHODOLOGY; NONLINEAR SYSTEM; SYSTEMS BIOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; SYSTEMS BIOLOGY;

EID: 84859187710     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.110     Document Type: Article

References (37)

1. H. Kitano, "Systems Biology: A Brief Overview," Science, vol. 295, no. 5560, pp. 1662-1664, 2002. (Pubitemid 34202893)
2. F. Horn and R. Jackson, "General Mass Action Kinetics," Archive for Rational Mechanics and Analysis, vol. 47, pp. 81-116, 1972.
3. D. Thieffry and R. Thomas, "Dynamical Behavior of Biological Regulatory Networks," Bull. of Math. Biology, vol. 57, no. 2, pp. 277-297, 1995.
4. H. de Jong et al., "Genetic Network Analyzer: Qualitative Simulation of Genetic Regulatory Networks," Bioinformatics, vol. 19, no. 3, pp. 336-344, 2003.
5. Y. Kaznessis, "Models for Synthetic Biology," BMC Systems Biology, vol. 1, no. 47, 2007.
6. S. Kay, Fundamentals of Statistical Signal Processing: Estimation Theory (volume 1), Prentice Hall, 1993.
7. M. Rodriguez-Fernandez et al., "A Hybrid Approach for Efficient and Robust Parameter Estimation in Biochemical Pathways," Biosystems, vol. 83, nos. 2/3, pp. 248-265, 2006. (Pubitemid 43199824)
8. P. Lindner and B. Hitzmann, "Experimental Design for Optimal Parameter Estimation of an Enzyme Kinetic Process Based on the Analysis of the Fisher Information Matrix," J. Theoretical Biology, vol. 238, no. 1, pp. 111-123, 2006. (Pubitemid 41737801)
9. D. Battogtokh et al., "Bifurcation Analysis of a Model of the Budding Yeast Cell Cycle," Chaos, vol. 14, no. 3, pp. 653-661, 2004. (Pubitemid 39443298)
10. D. Angeli et al., "Detection of Multistability, Bifurcations, and Hysteresis in a Large Class of Biological Positive-Feedback Systems," Proc. Nat'l Academy of Sciences USA, vol. 101, no. 7, pp. 1822-1827, 2004. (Pubitemid 38228975)
11. J. Lu, H.W. Engl, R. Machné, and P. Schuster, "Inverse Bifurcation Analysis of a Model for the Mammalian g1/s Regulatory Module," Proc. Int'l Conf. Bioinformatics Research and Development (BIRD '07), pp. 168-184, 2007. (Pubitemid 47290188)
12. T.A. Henzinger and H. Wong-Toi, "Using Hytech to Synthesize Control Parameters for a Steam Boiler," Proc. Formal Methods for Industrial Applications, pp. 265-282, 1995. (Pubitemid 126154447)
13. G. Frehse et al., "A Counterexample-Guided Approach to Parameter Synthesis for Linear Hybrid Automata," Proc. Int'l Workshop Hybrid Systems: Computation and Control (HSCC), pp. 187-200, 2008.
14. G. Batt et al., "Robustness Analysis and Tuning of Synthetic Gene Networks," Bioinformatics, vol. 23, no. 18, pp. 2415-2422, 2007. (Pubitemid 47423839)
15. B. Yordanov and C. Belta, "Parameter Synthesis for Piecewise Affine Systems from Temporal Logic Specifications," Proc. Int'l Workshop Hybrid Systems: Computation and Control, vol. 4981, pp. 542-555, 2008.
16. A. Donzé, B. Krogh, and A. Rajhans, "Parameter Synthesis for Hybrid Systems with an Application to Simulink Models," Proc. Int'l Conf. Hybrid Systems: Computation and Control (HSCC), pp. 165-179, 2009.
17. E.M. Clarke et al., Model Checking. MIT Press, 2000.
18. J.F. Guespin-Michel et al., "Epigenesis and Dynamic Similarity in Two Regulatory Networks in Pseudomonas Aeruginosa," Acta Biotheoretica, vol. 52, pp. 379-390, 2004. (Pubitemid 39459594)
19. L. Calzone, F. Fages, and S. Soliman, "BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge," Bioinformatics, vol. 22, no. 14, pp. 1805-1807, 2006. (Pubitemid 44288351)
20. P.T. Monteiro et al., "Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks," Bioinformatics, vol. 24, no. 16, pp. 227-233, 2008.
21. A. Rizk et al., "A General Computational Method for Robustness Analysis with Applications to Synthetic Gene Networks," Bioinformatics, vol. 25, no. 12, pp. i169-i178, 2009.
22. R. Donaldson and D. Gilbert, "A Model Checking Approach to the Parameter Estimation of Biochemical Pathways," Proc. Int'l Conf. Computational Methods in Systems Biology, pp. 269-287, 2008.
23. P. Collins et al., "Abstraction of Biochemical Reaction Systems on Polytopes," Proc. 18th IFAC World Congress, 2011.
24. G. Batt et al., "Efficient Parameter Search for Qualitative Models of Regulatory Networks Using Symbolic Model Checking," technical report, INRIA, 2010.
25. P. Ballarini et al., "Taming the Complexity of Biological Pathways through Parallel Computing," Briefings in Bioinformatics, vol. 10, no. 3, pp. 278-288, 2009.
26. J. Barnat, L. Brim, and D. Safránek, "High-Performance Analysis of Biological Systems Dynamics with the Divine Model Checker," Briefings in Bioinformatics, vol. 11, pp. 301-312, 2010.
27. A. Donzé et al., "Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology," Proc. RECOMB'09, pp. 155-169, 2009.
28. Z. Khalis et al., "The Smbionet Method for Discovering Models of Gene Regulatory Networks," Genes, Genomes and Genomics, vol. 3, no. 1, pp. 15-22, 2009.
29. B. Pal et al., "BUSpec: A Framework for Generation of Verification Aids for Standard Bus Protocol Specifications," Integration, the VLSI J., vol. 40, no. 3, pp. 285-304, 2007. (Pubitemid 46452829)
30. K. Hamaguchi et al., "Formal Verification of Speed-Dependent Asynchronous Circuits Using Symbolic Model Checking of Branching Time Regular Temporal Logic," Proc. Int'l Conf. Computer Aided Verification, pp. 410-420, 1991.
31. C. Chaouiya et al., "Logical Modelling of Regulatory Networks with Ginsim 2.3," Biosystems, vol. 97, no. 2, pp. 134-139, 2009.
32. G. Bernot et al., "Application of Formal Methods to Biological Regulatory Networks: Extending Thomas' Asynchronous Logical Approach with Temporal Logic," J. Theoretical Biology, vol. 229, no. 3, pp. 339-347, 2004. (Pubitemid 38844938)
33. T. Mestl et al., "A Mathematical Framework for Describing and Analysing Gene Regulatory Networks," J. Theoretical Biology, vol. 176, no. 2, pp. 291-300, 1995.
34. J. Barnat et al., "Parameter Scanning by Parallel Model Checking with Applications in Systems Biology," Proc. Ninth Int'l Workshop Parallel and Distributed Methods in Verification, and Second Int'l Workshop High Performance Computational Systems Biology (PDMC/ HiBi '10), pp. 95-104, 2010.
35. M. Swat, A. Kel, and H. Herzel, "Bifurcation Analysis of the Regulatory Modules of the Mammalian G1/S Transition," Bioinformatics, vol. 20, no. 10, pp. 1506-1511, 2004. (Pubitemid 39023153)
36. S. Liang, S. Fuhrman, and R. Somogyi, "Reveal, A General Reverse Engineering Algorithm for Inference of Genetic Network Architectures," Proc. Pacific Symp. Biocomputing, vol. 29, no. 3, pp. 18-29, 1998.
37. H. Ma, F. Boogerd, and I. Goryanin, "Modelling Nitrogen Assimilation of Escherichia Coli at Low Ammonium Concentration," J. Biotechnology, vol. 144, pp. 175-183, 2009.