Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

1. SBW
2. JDesigner
3. Jarnac
5. Matlab Interface
6. Optimization
6. Bifurcation
maintained by Frank Bergmann

High Performance Simulators


In an effort to create a fully SBML compliant simulator we have also developed a new simulator called roadRunner. Instead of interpreting model equations, roadRunner compiles the model equations dynamically, resulting in significant improvements in performance when compared with traditional simulators. roadRunner uses the integrator CVODE and NLEQ (ZIB 2003) for steady state analysis. To further speed up the simulation, the model is separated into a system of independent and dependent variables. This separation process is described in detail in (Vallabhajosyula et al. 2006). roadRunner has been written completely in C#. Provided that CVODE and NLEQ are available for a given operating system, roadRunner will run on that operating system. Thus, all major operating systems are supported. RoadRunner is published under the BSD license.

Availability: roadRunner is available as part of the Systems Biology Workbench. Source code can be obtained by request to Frank Bergmann.

-Frank Bergmann fbergman at u dot washington dot edu

sysbio/highperfsimulators.txt · Last modified: 2007/08/02 12:12 by mallain

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