Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

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

Jarnac: An Interactive Metabolic Systems Language

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SBW

Jarnac is only recommended for very experienced users. If you want a nice easy tool to do simulations then use JDesigner which comes with SBW

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Jarnac is a language for describing and manipulating cellular system models and can be used to describe metabolic, signal transduction and gene networks, or in fact any physical system which can be described in terms of a network and associated flows. Jarnac is basically version 2 of SCAMP.

Jarnac is based on a simple control language, similar to the Basic language and supports many of the constructs one would expect,  for loops, conditionals, while/do and repeat/until. It supports at least 7 different data types, including integers, floats, Booleans, strings, vectors, matrices and lists. Jarnac also supports user defined functions and external modules.

There is built-in computational support for: Dynamic simulation (using LSODAor CVODE integrator), steady state snalysis using the NLEQ solver, simple stability analysis (eigenvalues, using IMSL library), matrix arithmetic (All the main operators including things like transpose, det etc, using IMSL library), Metabolic Control Analysis (All steady state control coefficients and elasticities), Metabolic atructural analysis (Null space and conservation relation analysis with others to follow), stochastic Simulation (using standard Gillespie method).

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