Taming the complexity of biological pathways through parallel computing

Briefings in Bioinformatics

Volumn 10, Issue 3, 2009, Pages 278-288

  Ballarini, Paolo ^a,b,c,f   Guido, Rosita ^d   Mazza, Tommaso ^a,e   Prandi, Davide ^a,e  

^a CoSBi centre ^*  (Italy)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

^d UNIVERSITY OF CALABRIA   (Italy)

^e UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^f UNIVERSITY OF TRENTO   (Italy)

Author keywords

Biological pathways; Model checking; ODE numerical solutions; Parallel computing; Stochastic simulation

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SIMULATION; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; STOCHASTIC MODEL; SYSTEMS BIOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MODELS, BIOLOGICAL; SOFTWARE; STOCHASTIC PROCESSES; SYSTEMS INTEGRATION;

EID: 65549164378     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbp020     Document Type: Article

References (63)

1. Kitano H. Foundations of Systems Biology. USA: MIT Press, 2001.
2. Grama A, Gupta A, Karypis G, et al. Introduction to Parallel Computing: Design and Analysis of Algorithms. San Francisco, CA, USA: Pearson Education, 2003.
3. Reinders J. Intel Threading Building Blocks. CA, USA: O'Reilly & Associates, 2007.
4. Leirson C. Cilk++: Multicore-Enabling Legacy C++ Code. USA: Carnegie Mellon University Parallel Thinking Series, 2008.
5. Shirts M, Pande V. Screen savers of the world unite! Science 2000;5498:1903-4.
6. Anderson D. BOINC: A system for public-resource computing and storage. In: Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing. Pittsburgh, USA, November 8, 2004;4-10.
7. Chamberlain B. Graph partitioning algorithms for distributing workloads of parallel computations. Technical Report UW-CSE-98-10, University of Washington, 1998.
8. Burrage K. Parallel and Sequential Methods for Ordinary Differential Equations. USA: Oxford University Press, 1995.
9. Butcher JC. Numerical Methods for Ordinary Differential Equations. USA: John Wiley and Sons, 2003.
10. Dongarra JJ, Duff IS, Sorensen DC, et al. Numerical Linear Algebra for High-performance Computers. USA: SIAM, 1998.
11. Clementis A, Dodero G, Giannuzzi V. A practical approach to efficient use of heterogeneous PC network for parallel mathematical computation. In: Proceedings of the 9th International Conference on High-Performance Computing and Networking (HPCN Europe 2001). Amsterdam, The Netherlands, 2001.
12. Van de Geijn RA. Using PLAPACK: Parallel Linear Algebra Package. USA: MIT Press, 1997.
13. Nieploch J, Harrison RJ, Littlefield RJ. Global arrays: A nonuniform memory access programming model for high-performance computers. J Supercomput 1996;10: 169-89.
14. Aouad LM, Petiton SG, Sato M. Grid and duster matrix computation with persistent storage and out-of-core programming. In: Proceedings of the 6th IEEE International Conference on Cluster Computing (CLUSTER 2005). Boston, MA, USA, 2005.
15. Amodio P, Brugnano L. Parallel solution in time of ODEs: Some achievements and perspectives. Appl Numer Math 2009;59 424-35.
16. Burrage K. Parallel methods for ODEs. Adv Comput Math 1997;7 1-31.
17. Hindmarsh AC, Brown PN, Grant KE, et al. SUNDIALS: Suite of nonlinear and differential/algebraic equation solvent ACM Trans Math Soft 2005;31:363-96.
18. Bendtsen C. A parallel stiff ODE solver based on MIRKs. Adv Comput Math 1997;7:27-36.
19. Amodio P, Brugnano L. ParalleloGAM: A parallel code for ODEs. Appl Numer Math 1998;28:95-106.
20. Bergmann FT, Herbert SM. SBW - a modular framework for systems biology. In: Proceedings of the 38th Winter Simulation Conference (WSC'06). Monterey, CA, USA, 2006.
21. Osana Y, Fukushima T, Yoshimi M, et al. A framework for ODE-based multimodel biochemical simulations on an FPGAs. In: International Conference on Field Programmable Logic and Applications (FLP 2005). Tampere, Finland, 2005.
22. Owens J, Luebke D, Govindaraju N, et al. A survey of general-purpose computation on graphics hardware. Comput Graph Forum 2007;1:80-113.
23. Shilling CH, Letsher D, Palsson B. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 2000;203:229-48.
24. Lee L-Q, Varner J, Ko K. Parallel extreme pathway computation for metabolic networks. In: Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB'04). Staford, CA, USA, 2004.
25. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem A 1977;81:2340-61.
26. De Jong H. Modeling and simulation of genetic regulatory systems: A literature review. J Comput Biol 2002;9:67-103.
27. Gillespie DT. A rigorous derivation of the chemical master equation. Physica A 1992;188:404-25.
28. Gibson MA, Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 2000; 112:1876-89.
29. Takahashi K, Vel Arjunan SN, Tomita M. Space in systems biology of signaling pathways: Towards intracellular molecular crowding in silico. FEBS Lett 2005;579:1783-8.
30. Elf J, Ehrenberg M. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. IEE Systems Biol 2004;1:230-6.
31. Dematte' L, Mazza T. On parallel stochastic simulation of diffusive systems. In: Proceedings of the 6th International Conference on Computational Methods in Systems Biology (CMSB2008). LNBI 2008; 5307:191-210.
32. Fedoroff N, Fontana W. GENETIC NETWORKS: Small numbers of big molecules. Science 2002;297:1129-30.
33. Tian T, Burrage K. Parallel implementation of stochastic simulation for large-scale cellular processes. In: Proceedings of the 8th International Conference on High-Performance Computing in Asia-Pacific Region. Beijing, China, 2005.
34. Burrage K, Burrage P, Jeffrey S, et al. A GRID implementation of chemical kinetic simulation methods in genetic regulation. In: Proceedings of the Conference on Advanced Computing, Grid Applications and eResearch (APAC03). Gold Coast, Australia, 2003.
35. Jun-qing N, Hao-ran Z, Jiu-sheng C, et al. A distributed-based stochastic simulation algorithm for large biochemical reaction networks. In: Proceedings of the 1st International Conference on Bioinformatics and Biomedical Engineering. Wuhan, China, 2007.
36. Schwehm M. Parallel stochastic simulation of whole-cell models. In: Proceedings of International Conference on Architecture of Computing Systems. ARCS 2002. Trends in Network and Pervasive Computing, Workshop Proceedings. Karlsruhe, Germany, 2002.
37. Jeschke M, Park A, Ewald R, et al. Parallel and distributed spatial simulation of chemical reactions. In: Proceedings of the 22nd Workshop on Principles of Advanced and Distributed Simulation (PADS08) Rome, Italy, 2008.
38. Meredith JS, Alam SR, Vetter JS. Analysis of a computational biology simulation technique on emerging processing architectures. In: Proceedings of the 21th International Parallel and Distributed Processing Symposium (IPDPS 2007). Long Beach, California, USA, 2007.
39. Salwinski L, David E. In silico simulation of biological network dynamics. Nat Biotechnol 2004;22:1017-19.
40. Li H, Petzold L. Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit. Santa Barbara: Department of Computer Science, University of California, 2007.
41. Clarke EM, Grumberg O, Peled DA. Model Checking. USA: Springer, 1999.
42. Pnueli A. The temporal logic of programs. In: Proceedings of the 18th IEEE Symposium on Foundations of Computer Science. Providence, Rhode Island, USA, October 31-November 2, 1977, 46-67.
43. Batt G, Ropers, D, de Jong H, et al. Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics 2005;21:19-28.
44. Calzone L, Fages F, Soliman S. BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 2006;22:1805-7.
45. Hansson H, Jonsson B. A logic for reasoning about time and reliability. Formal Aspects Comput 1994;6:512-35.
46. Aziz A, Kumud S, Vigyan S, et al. Model checking continuous time Markov chains. ACM Trans Comput Logic 1996;1:162-70.
47. Baier C, Haverkort B, Hermanns H, et al. Model-checking algorithms for continuous-time Markov chains. IEEE Trans Software Eng 2003; 29:524-41.
48. Stewart WJ. Introduction to the Numerical Solution of Markov Chains New Jersey, USA: Princeton, 1994.
49. Heath J, Kwiatkowska M, Norman G, et al. Probabilistic model checking of complex biological pathways. Theor Comput Sci 2007; 391:239-57.
50. Ballarini P, Csikasz-Nagy A, Mazza T, et al. Studying irreversible transitions in a model of cell cycle regulation. In: Proceedings of the 3rd International Workshop on Practical Applications of Stochastic Modelling (PASM 2008). Palma de Mallorca, Spain, 2008. vol. 232, 39-53.
51. Ciochetta F, Gilmore S, Guerriero ML, et al. Integrated simulation and model-checking for the analysis of biochemical systems. In: Proceedings of the 3rd International Workshop on Practical Applications of Stochastic Modelling (PASM 2008). Palma de Mallorca, Spain, 2008.
52. Bhat G, Cleaveland R, Grumberg O. Efficient on-the-fly model checking for CTL. In: Proceedings of the 10th Annual IEEE Symposium on Logic in Computer Science (LICS'95). San Diego, CA, USA, 1995.
53. Holzmann GJ. The Spin Model Checker. USA: Addison-Wesley, 2003.
54. Baier C, Katoen JP. Principles of Model Checking. USA: MIT press, 2008.
55. NuSMV symbolic model checker, http://nusmv.irst.itc.it/ (March 2009, date last accessed)
56. PRISM model checker, http://www.prismmodelchecker.org/ (March 2009, date last accessed)
57. Barnat J, Brim L, Cerna I, et al. Parallel model checking large-scale genetic regulatory networks with DiVinE. Electronic Notes Theor Comput Sci 2008;194:35-50.
58. Courcoubetis C, Vardi M, Wolper P, et al. Memory-efficient algorithms for the verification of temporal properties. Form Method Syst Des 1992;1:275-88.
59. Holzmann GJ, Peled D, Yannakakis M. On nested depth first search. In: Gregoire J-C, Gerard HJ, Doron PA, (eds). DIMACS: Series in Discrete Mathematics and Theoretical Computer Science. USA: AMS Bookstore, 1996.
60. Brim L, Černá I, Krčál P, et al. Distributed LTL model checking based on negative cycle detection. In: Proceedings of the 21st Foundations of Software Technology and Theoretical Computer Science (FST TCS 2001). Bangalore, India, 2001.
61. Brim L, Černá I, Krčál P, et al. DiVinE - a tool for distributed verification. In: Proceedings of the 18th Computer Aided Verification (CAV 2006). Seattle, WA, USA, 2006.
62. Ciardo G. Distributed and structured analysis approaches to study large and complex systems. In: Proceedings of Lectures on Formal Methods and performance Analysis: First EEF/Euro Summer School on Trends in Computer Science. Berg En Dal, The Netherlands, 2001.
63. Kwiatkowska M, Parker D, Zhang Y, et al. Dual-processor parallelisation of symbolic probabilistic model checking. In: Proceedings of the 12th International Symposium on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS'04) Volendam, The Netherlands, 2004.