E-CELL: Software environment for whole-cell simulation

Bioinformatics

Volumn 15, Issue 1, 1999, Pages 72-84

  Tomita, Masaru ^a   Hashimoto, Kenta ^a   Takahashi, Kouichi ^a   Shimizu, Thomas Simon ^a,c   Matsuzaki, Yuri ^a   Miyoshi, Fumihiko ^a   Saito, Kanako ^a   Tanida, Sakura ^a   Yugi, Katsuyuki ^a   Venter, J Craig ^b   Hutchison III, Clyde A ^b  

^a KEIO UNIVERSITY   (Japan)

^b J CRAIG VENTER INSTITUTE   (United States)

^c Department of Zoology ^*  (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOCHEMISTRY; BIOENGINEERING; CELL FUNCTION; COMPUTER PROGRAM; GENOME; INFORMATION SCIENCE; KINETICS; MOLECULAR GENETICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION;

EID: 0033031386     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.1.72     Document Type: Article

References (24)

1. Arita, M., Hagiya, M. and Shiratori, T. (1994) GEISHA SYSTEM: an environment for simulating protein interaction. In Takagi, T. (ed.), Proceedings, Genome Informatics Workshop 1994. Universal Academy Press, Tokyo, pp. 81-89.
2. Barkai, N. and Leibler, S. (1997) Robustness in simple biochemical networks. Nature, 387, 913-917.
3. Barshop, B.A., Wrenn, R.F. and Frieden, C. (1983) Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible, portable system. Anal. Biochem., 130, 134-145.
4. Bray, D. (1998) SIGNALING COMPLEXES: Biophysical constraints on intracellular communication. Annu. Rev. Biophys. Biomol. Struct., 27, 59-75.
5. Bray, D., Bourret, R.B. and Simon, M.I. (1993) Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Mol. Biol. Cell, 4, 469-482.
6. Cornish-Bowden, A. and Hofmeyr, J.H. (1991) MetaModel: a program for modeling and control analysis of metabolic pathways on the IBM PC and compatibles. Comput. Applic. Biosci., 7, 89-93.
7. Dang, Q. and Frieden, C. (1997) New PC versions of the kinetic-simulation and fitting programs, KINSIM and FITSIM. Trends Biochem. Sci., 22, 317.
8. Ehlde, M. and Zacchi, G. (1995) MIST: a user-friendly metabolic simulator. Comput. Applic. Biosci., 11, 201-207.
9. Fleischmann, R.D. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
10. Fraser, C.M. et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science, 270, 397-403.
11. Galper, A.R., Brutlag, D.L. and Millis, D.H. (1993) Knowledge-based simulation of DNA metabolism: prediction of action and envisionment of pathways. In Hunter, L. (ed.). Artificial Intelligence and Molecular Biology. AAAI Press/The MIT Press, CA/MA, pp. 429-436.
12. Kanehisa, M. (1996) Toward pathway engineering: a new database of genetic and molecular pathways. Sci. Technol. Jpn. 59, 34-38.
13. Karp, P.D. (1993) A qualitative biochemistry and its application to the regulation of the tryptophan operon. In Hunter, L. (ed.), Artificial Intelligence and Molecular Biology. AAAI Press/The MIT Press, CA/MA, pp. 289-324.
14. Karp, P.D., Riley, M., Paley, S.M. and Pelligrini-Toole, A. (1996) Eco-Cyc: encyclopedia of E.coli genes and metabolism. Nucleic Acids Res., 24, 32-40.
15. Kuipers, B. (1986) Qualitative simulation. Artif. Intell., 29, 289-338.
16. McAdams, H.H. and Shapiro, L. (1995) Circuit simulation of genetic networks. Science, 269, 650-656.
17. Mendes, P. (1993) GEPASI: a software package for modeling the dynamics, steady states and control of biochemical and other systems. Comput. Applic. Biosci., 9, 563-571.
18. Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci., 22, 361-363.
19. Meyers, S. and Friedland, P. (1984) Knowledge-based simulation of genetic regulation in bacteriophage lambda. Nucleic Acids Res., 12, 1-9.
20. Mushegian, A.R. and Koonin, E.V. (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA, 93, 10268-10273.
21. Novak, B. and Tyson, J.J. (1995) Quantitative analysis of a molecular model of mitotic control in fission yeast. J. Theor. Biol., 173, 283-305.
22. Sauro, H.M. (1993) SCAMP: a general-purpose simulator and metabolic control analysis program. Comput. Applic. Biosci., 9, 441-450.
23. Segel, I.H. (1975) Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State Enzyme Systems. John Wiley & Sons. New York.
24. Tyson, J.J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc. Natl Acad. Sci. USA. 88. 7328-7332.