BioSim - A New Qualitative Simulation Environment for Molecular Biology

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology, ISMB 1998

Volumn , Issue , 1998, Pages 85-94

  Heidtke, Keirsten R ^a   Schulze Kremer, Steffen ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTATION THEORY; DIFFERENTIAL EQUATIONS; KNOWLEDGE BASED SYSTEMS; MOLECULAR BIOLOGY; PROLOG (PROGRAMMING LANGUAGE);

BIOCHEMICAL SYSTEMS; BIOLOGICAL PROCESS; LOGIC-PROGRAMMING; PROGRAMMING TECHNIQUE; QUALITATIVE REASONING; QUALITATIVE SIMULATION; QUANTITATIVE INFORMATION; REASONING METHODS; REGULATORY PROCESS; SIMULATION ENVIRONMENT;

LOGIC PROGRAMMING;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; COMPUTER LANGUAGE; COMPUTER PROGRAM; COMPUTER SIMULATION; GLYCOLYSIS; LOGIC; MOLECULAR BIOLOGY; PHYSIOLOGY;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; GLYCOLYSIS; LOGIC; MODELS, BIOLOGICAL; MOLECULAR BIOLOGY; PROGRAMMING LANGUAGES; SOFTWARE;

EID: 0031604093     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (31)

1. Aggoun, A.; Chan, D.; Dufresne, P.; Falvey, E.; Grant, H.; Herold, A.; MacCartney, G.; Meier, M.; Miller, D.; Mudambi, S.; Perez, B.; van Rossum, E.; Schimpf, J.; Tsahageas, P. A.; and de Villeneuve, D. H. 1995. Eclipse 3.5 user manual, http://www.ecrc.de/eclipse/eclipse.html.
2. Artoli, E.; Avanzolini, G.; MarteUi, L.; and Ursino, M. 1996. An expert system based on causal knowledge: validation on post-cardiosurgical patients. International Journal of Bio-Medical Computing 41:19 - 37.
3. Brisset, P.; Prüwirth, T.; Gervet, C; and L i m, P. 1995. Eclipse 3.5 extension user manual. http://www.ecrc.de/eclipse/eclipse.html.
4. Brutlag, D. L.; Galper, A. R.; and Millis, D. H. 1991. Knowledge-Based Simulation of DNA Metabolism: Prediction of Enzyme Action. Computer Applications in Biosciences 7(1):9 - 19.
5. Clancy, D. J., and Kuipers, B. 1997. Model decomposition and simulation: A component beised qualitative simulation algorithm. In The lĄth National Conference on Artificial Intelligence (AAAI-97). Rhode I s land: A A AI Press.
6. Crawford, J.; Farquhar, A.; and Kuipers, B. 1990. QPC: A compiler from physical models into qualitative differential equations. In Proc. 8th National Conf. on Artificial Intelligence (AAAI-90), 365-372. San Mateo, CA: Morgan Kaufinćuin.
7. Dague, P. 1995. Quahtative reasoning: A survey of techniques and applications. AI Communications 8(3/4):119 - 192.
8. Davis, E. 1990. Order of magnitude reasoning in qualitative differential equations. In Weld, D. S., and de Kleer, J., eds.. Readings in Qualitative Reasoning about Physical Systems. San Mateo, CA: Morgan Kaufmann. 422-434.
9. Forbus, K. D. 1984. Qualitative process theory. Artificial Intelligence 24:85-168.
10. Forbus, K. D. 1990. The quahtative process engine. In Weld, D. S., and de Kleer, J., eds.. Readings in Qualitative Reasoning about Physical Systems. San Mateo, CA: Morgan Kaufmann. 220-235. http://www.cs.cmu.edu/afs/cs/project/ciirepository/ai/axeas/reasoimg/qualittv/qpe/O.html.
11. Frühwirth, T.; Herold, A.; Küchenhoff, V.; Provost, T. L.; Lim, P.; Monfroy, E.; and Wallace, M. 1992. Constraint logic programming - an informal introduction. In Comyn, G., ed.. Logic Pragrammming in Action: Second International Logic Programming Summer School, volume 636. Zürich: Springer-Verlag. 3¬ 35. Springer Lecture Notes.
12. Heidtke, K. R., and Schulze-Kremer, S. 1997. Qualitative reeisoning on gene control and reproduction demonstrated on A phage growth. In Prishman, D., and Mewes, H. W., eds.. Proceedings of the German Conference on Bioinformatics GCB'97, 37-40. MIPS-GSF Martinsried.
13. Heidtke, K. R., and Schulze-Kremer, S. 1998. Design and implementation of a qualitative simulation model of A phage infection. Bioinformatics. in press.
14. Karp, P. D., and Mavrovouniotis, M. M. 1994. Representing, analayzing, and synthesizing biochemical pathways. I E E E Expert 9(2): 11 - 22.
15. Karp, P. D.; Riley, M.; Paley, S.; Pellegrini-Toole, A.; and Krummenacker, M. 1997. EcoCyc: Encyclopedia of E. coli genes and metabolism. Nucleic Acids Research 25(1):43 - 50.
16. Karp, P. D. 1993. A qualitative biochemistry and its application to the tryptophan operon. In Hunter, L., ed., Artificial Intelligence and Molecular Biology, 289 - 324. A A A I Press.
17. Kazic, T. 1993a. Reasoning about biochemical compounds and processes. In H.A. Lim, J.W. Fickett, C. C, and Robbins, R., eds., Second International Conference on Bioinformatics, Supercomputing and the Human Genome Project, 35 - 49. Singapore: World Scientific.
18. Kazic, T. 1993b. Representation, reasoning and the intermediary metabolism of E. coli. In T. N. Mudge, V. M., and Hunter, L., eds., Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, volume 1, 853 - 862. Los Alamitos, C A: I E E E Computer Society Press.
19. Kuipers, B., and Kassirer, J. 1987. Knowledge acquisition by analysis of verbatim protocols. In Kidd, A., ed.. Knowledge Acquisition for Expert Systems, volume 29, 289 - 338.
20. Kuipers, B. 1986. Qualitative simulation. Artificial Intelligence 29:289 - 338.
21. Kuipers, B. 1994. Qualitative Reasoning. Modeling and Simulation with Incomplete Knowledge. Cambridge, MA: M I T Press, http://www.cs.utexas.edu/users/qr/QR-software.html.
22. Mavrovouniotis, M. L., and Stephanopoulos, G. 1990. Formal order-of-magnitude reasoning in process engineering. In Weld, D. S., and de Kleer, J., eds., Readings in Qualitative Reasoning about Physical Systems. San Mateo, C A: Morgan Kaufmann. 327-336.
23. McAdams, H. H., and Shapiro, L. 1995. Circuit simulation of genetic networks. Science 269:650-656. Meyers, S., and Friedland, P. 1984. Knowledge based simulation of genetic regulation in bacteriophage lambda. Nucleic Acids Research 12(1):l-9.
24. Schulze-Kremer, S. 1990. CS-Prolog Parallel Programming in Logic with Transputers. Apphcation: MolSIM, a Program for Simulation of Concurrent MolecularbiologicalProcesses. In Turner, S. J., ed., 12. OUG Conference, Exeter, Tools and Techniques for Transputer Applications, 97 -110. Amsterdam: IOS Press.
25. Schulze-Kremer, S. 1995. Molecular Bioinformatics: Algorithms and Applications. Berlin, New York: de Gruyter.
26. Shimada, T.; Hagiya, M.; Arita, M.; Nishizaki, S.; and Tan, C. 1995. Knowledge-liased Simulation of Regulatory Action in Lambda Phage. International Journal of Artificial Intelligence Tools 4(4):511-524.
27. Teleki, L. 1996. Constraint logic programming: A framework for qualitative reasoning. In Proceedings of the Tenth International Workshop on Qualitative Reasoning.
28. Thomas, R. 1991. Regulatory Networks Seen as Asynchronous Automata: A Logical Description. Journal of Theoretical Biology 153:1 - 23.
29. Ursino, M.; Avanzolìni, G.; and Barbini, P. 1992. Qualitative simulation of dynamic physiological models using the KEE environment. Artificial Intelligence in Medicine 4:53 - 73.
30. Ursino, M.; Artioü, E.; Avanzolini, G.; and Potuto, V. 1994. Integration of quantitative and qualitative reasoning: an expert system for cardiosurgical patients. Artificial Intelligence in Medicine 6:229 - 247.
31. Weld, D. S., and de Kleer, J. 1990. Readings in Qualitative Reasoning About Physical Systems. San Mateo, CA: Morgcm Kaufmann.