Biomolecular network simulator: Software for stochastic simulation of cellular biological processes

Agent Directed Simulation Symposium, ADS 2007 - Proceedings of the 2007 Spring Simulation Multiconference, SpringSim 2007

Volumn , Issue , 2007, Pages 345-349

  Chushak, Yaroslav ^a   Foy, Brent ^b   Frazier, John ^c  

^a U S ARMY MEDICAL RESEARCH AND MATERIEL COMMAND   (United States)

^b WRIGHT STATE UNIVERSITY   (United States)

^c AIR FORCE RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY; C (PROGRAMMING LANGUAGE); COMPUTER SOFTWARE; GRAPHICAL USER INTERFACES; MONTE CARLO METHODS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS; USER INTERFACES;

BIOCHEMICAL REACTIONS; BIOMOLECULAR REACTIONS; MODEL AND SIMULATION; MONTE CARLO TRAJECTORIES; MULTI PROCESSOR ARCHITECTURE; SIMULATION ANALYSIS; STOCHASTIC SIMULATION ALGORITHMS; STOCHASTIC SIMULATIONS;

MATLAB;

EID: 67650769717     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (6)

1. Voit, E. O., 2000. Computational Analysis of Biochemical Systems. Cambridge University Press, Cambridge, UK.
2. Elowitz, M. B., Levine, A. J., Siggia, E. D., and Swain, P. S., 2002, "Stochastic Gene Expression in a Single Cell." Science, v.297, no. 5584, (August): 1183-1186.
3. Kaern, M., Elston, T. C., Blake, W. J, and Collins, J. J., 2005, "Stochasticity in Gene Expressions: From Theories to Phenotypes." Nature Reviews Genetics, v. 6, no, 6 (June): 451-464.
4. Gillespie, D., 1977, "Exact Stochastic Simulation of Coupled Chemical Reactions." J. Phys. Chem. v. 81: 2340-2361.
5. Huska, M., Finney, A., Sauro H. M., Bolouri, H. et al., 2003, "The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models." Bioinformatics, v. 19, no. 4: 524-531.
6. Kepner, J., 2001, "Parallel Programming with Matlab- MPI." Proceedings of the High Performance Embedded Computing workshop, HPEC 2001, (Lexington, MA, Sep 25-27) MIT Lincoln Laboratory.