Jarnac: An Interactive Metabolic Systems Language
Downloads
Jarnac 2.0 Production Version #5
Documentation
Jarnac 2.0 Documentation (PDF)
Sample Models
Jarnac is only recommended for very experienced
users. If you want a nice easy tool to do
simulations then use JDesigner
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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).
Notices
YOU MUST USE THE LATEST JARNAC 2.0 for versions 1.8+. When you install Jarnac make sure you RE-REGISTER Jarnac with SBW. Go to the options menu and select register with SBW. Then QUIT and RESTART SBW. To restart SBW, stop it first then restart it (see System Biology Workbench menu in start menu).
Version History
Screen Shots
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