Executable biology

Proceedings - Winter Simulation Conference

Volumn , Issue , 2006, Pages 1675-1682

  Fisher, Jasmin ^a   Henzinger, Thomas A ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SYSTEMS; BIOLOGY; COMPUTATIONAL COMPLEXITY; COMPUTER SCIENCE; ENGINEERING RESEARCH; MATHEMATICAL MODELS;

(ALGORITHMIC) COMPLEXITY; BIOLOGICAL MODELLING; BIOLOGICAL PHENOMENA; BIOLOGICAL RESEARCH; BIOLOGICAL TECHNIQUES; COMPUTATIONAL MODELLING; COMPUTATIONAL MODELS; ENGINEERING DISCIPLINES; MAINSTREAM (MS); TWO TYPES;

FORMAL LOGIC;

EID: 34249683449     PISSN: 08917736     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/WSC.2006.322942     Document Type: Conference Paper

References (50)

1. Alon, U., M.G. Surette, N. Barkai, and S. Leibler. 1999. Robustness in bacterial Chemotaxis. Nature 397:168-71.
2. Alur, R., C. Belta, F. Ivancic, V. Kumar, M. Mintz, G. Pappas, H. Rubin, and J. Schug. 2001. Hybrid modeling and simulation of biomolecular networks. In Hybrid Systems: Computation and Control (HSCC), LNCS 2034:19-32. Springer.
3. Alur, R., T.A. Henzinger, G. Lafrerriere, and G.J. Pappas. 2000. Discrete abstractions of hybrid systems. Proceedings of the IEEE 88:971-984.
4. Antoniotti, M., B. Mishra, C. Piazza, A. Policriti, and M. Simeoni. 2004. Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice. Theoretical Computer Science 325:45-67.
5. Barjis, J., and I. Barjis. 1999. Formalization of the protein production by means of Petri nets. In Proceedings of the International Conference on Information Intelligence and Systems (ICIIS), 4-9. IEEE.
6. Bray, D., M.D. Levin, and C.J. Morton-Firth. 1998. Receptor clustering as a cellular mechanism to control sensitivity. Nature 393:85-88.
7. Brown, K.S., and J.P. Sethna. 2003. Statistical mechanical approaches to models with many poorly known parameters. Physical Review E 68.
8. Burstein, Z. 1995. A network of model of developmental gene hierarchy. Journal of Theoretical Biology 174:1-11.
9. Calder, M., V. Vyshemirsky, D. Gilbert, and R. Orton. 2005. Analysis of signaling pathways using the PRISM model checker. In Computational Methods in Systems Biology (CMSB), 179-190.
10. Cardelli, L. 2004. Brane calculi. In Computational Methods in Systems Biology (CMSB), LNCS 3082:257-278. Springer.
11. Cardelli, L. 2005. Abstract machines of systems biology. Transactions on Computational Systems Biology 3:145-168.
12. Clarke, E.M., O. Grumberg, and D. Peled. 1999. Model Checking. MIT Press.
13. Curti, M., P. Degano, C. Priami, and C. Baldari. 2004. Modeling biochemical pathways through enhanced pi-calculus. Theoretical Computer Science 325: 111-140.
14. Damm, W., and D. Harel. 2001. LSCs: Breathing life into message sequence charts. Formal Methods in System Design 19:45-80.
15. de Jong, H., J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, and J. Geiselmann. 2003. Hybrid modeling and simulation of genetic regulatory networks: A qualitative approach. In Hybrid Systems: Computation and Control (HSCC), LNCS 2623:267-282. Springer.
16. Dill, D., M. Knapp, P. Gage, C. Talcott, K. Laderoute, and P. Lincoln. 2005. The pathalyzer: A tool for analysis of signal transduction pathways. In Recomb Satellite Workshop on Systems Biology.
17. Efroni, S., D. Harel, and I.R. Cohen. 2003. Toward rigorous comprehension of biological complexity: Modeling, execution, and visualization of thymic T-cell maturation. Genome Research 13:2485-97.
18. Efroni, S., D. Harel, and I.R. Cohen. 2005. Reactive animation: Realistic modeling of complex dynamic systems. IEEE Computer 38:38-47.
19. Errampalli, D.D., C. Priami, and P. Quaglia. 2004. A formal language for computational systems biology. OMICS 8:370-80.
20. Fisher, J., D. Harel, E.J. Hubbard, N. Piterman, M.J. Stern, and N. Swerdlin. 2004. Combining state-based and scenario-based approaches in modeling biological systems. In Computational Methods in Systems Biology (CMSB), LNCS 3082:236-241. Springer.
21. Fisher, J., N. Piterman, E.J. Hubbard, M.J. Stern, and D. Harel. 2005. Computational insights into Caenorhabditis elegans vulval development. Proceedings of the National Academy of Sciences. USA 102:1951-6.
22. Fisher, J., N. Piterman, A. Hajnal, and T.A. Henzinger. 2006a. Predictive modeling of C. elegans vulval development. Submitted.
23. Fisher, J., N. Piterman, and T.A. Henzinger. 2006b. Bounded asynchrony: A notion of concurrency tailored for modeling cell-cell interactions. Submitted.
24. Ghosh, R., A. Tiwari, and C. Tomlin. 2003. Automated symbolic reachability analysis with application to delta-notch signaling automata. In Hybrid Systems: Computation and Control (HSCC), LNCS 2623:233-248. Springer.
25. Ghosh, R., and C. Tomlin. 2001. Lateral inhibition through delta-notch signaling: A piecewise affine hybrid model. In Hybrid Systems: Computation and Control (HSCC), LNCS 2034:232-246. Springer.
26. Gilman, A., and A.P. Arkin. 2002. Gentic code: Representations and dynamical models of genetic components and networks. Annual Reviews of Genomics and Human Genetics 3:341-69.
27. Harel, D. 1987. Statecharts: A visual formalism for complex systems. Science of Computer Programming 8:231-274.
28. Harel, D. 2002. A grand challenge for computing: Towards full reactive modeling of a multi-cellular animal. The Bulletin of the European Association for Theoretical Computer Science (EATCS) 81:226-235.
29. Henzinger, T.A. 1996. The theory of hybrid automata. In Logic in Computer Science (LICS), 278-292. IEEE.
30. Hu, J., W.C. Wu, and S. Sastry. 2004. Modeling subtilin production in bacillus subtilis using stochastic hybrid systems. In Hybrid Systems: Computation and Control (HSCC), LNCS 2993:417-431. Springer.
31. Kaern, M., T.C. Elston, WJ. Blake, and J.J. Collins. 2005. Stochasticky in gene expression: From theories to phenotypes. Nature Reviews Genetics 6:451-64.
32. Kam, N., D. Harel, and I.R. Cohen. 2001. The immune system as a reactive system: Modeling T-cell activation with Statecharts. In Proceedings of Visual Languages and Formal Methods (VLFM), 15-22. IEEE.
33. Kam, N., D. Harel, H. Kugler, R. Marelly, A. Pnueli, E.J.A. Hubbard, and MJ. Stern. 2003. Formal modeling of C. elegans development: A scenario-based approach. In Computational Methods in Systems Biology (CMSB), LNCS 2602:4-20. Springer.
34. Lazebnik, Y. 2002. Can a biologist fix a radio? Cancer Cell 2: 179-82.
35. Li, F., T. Long, Y. Lu, Q. Ouyand, and C. Tang. 2004. The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences USA 101:4781-6.
36. Lincoln, P., and A. Tiwari. 2004. Symbolic systems biology: Hybrid modeling and analysis of biological networks. In Hybrid Systems: Computation and Control (HSCC), LNCS 2993:417-431. Springer.
37. Marnellos, G., and E. Mjolsness. 1998. A gene network approach to modeling early neurogenesis in Drosophila. In Pacific Symposium on Biocomputing, 30-41.
38. McAdams, H.H., and L. Shapiro. 1995. Circuit simulation of genetic networks. Science 269:650-6.
39. Milner, R. 1971. An algebraic definition of simulation between programs. In International Joint Conferences on Artificial Intelligence (IJCAI), 481-489. British Computer Society.
40. Milner, R. 1999. Communicating and Mobile Systems: The pi-Calculus. Cambridge University Press.
41. Priami, C. 1995. The stochastic pi-calculus. Comp. J. 38:578-589.
42. Priami, C., A. Regev, E.Y. Shapiro, and W. Silverman. 2001. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80:25-31.
43. Regev, A., E.M. Panina, W. Silverman, L. Cardelli, and E.Y. Shapiro. 2004. Bioambients: An abstraction for biological compartments. Theoretical Computer Science 325:141-167.
44. Regev, A., W. Silverman, and E.Y. Shapiro. 2001. Representation and simulation of biochemical processes using the pi-calculus process algebra. In Pacific Symposium on Biocomputing, 459-70.
45. Rosenfeld, N., T.J. Perkins, U. Alon, M.B. Elowitz, and P.S. Swain. 2006. A fluctuation method to quantify in vivo fluorescence data. Biophysical Journal 91: 645-54.
46. Rutten, J., M. Kwiatkowska, G. Norman, and D. Parker. 2004. Mathematical techniques for analyzing concurrent and probabilistic systems, Volume 23 of CRM Monograph Series. American Mathematical Society.
47. Sadot, A., J. Fisher, D. Barak, Y. Admanit, MJ. Stern, E.J.A. Hubbard, and D. Harel. 2006. Towards verified biological models. Submitted.
48. Shmulevitch, I., R. Dougherty, S. Kim, and W. Zhang. 2002. Probabilistic boolean networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-74.
49. Sprinzak, D., and M.B. Elowitz. 2005. Reconstruction of genetic circuits. Nature 438:443-8.
50. Sternberg, P., and H. Horvitz. 1989. The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans. Cell 58:679-93.