Computational Systems Biology
Sauro Lab
University of Washington
Home  |   Downloads  |   News  |   Research  |   Papers  |   About Us  |   Contact Us  |   SBW Help   |   Jobs

What is SBW 
Research Impact 
Published Papers 
Lab Members 
Available Positions 
CSB Links 
Student Projects 
Software Downloads:

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

Jarnac: An Interactive Metabolic Systems Language


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

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.

Within the SBW framework Jarnac acts as both a script engine for model building, simulation, and analysis, and a simulation engine for SBML files. Jarnac is able to perform continuous and stochastic simulations.

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).

Sceen Shots


Jarnac is installed with SBW. For more information see the SBW installation page.

Jarnac is currently only supported on Windows.

Documentation & Help

sysbio/jarnac.txt · Last modified: 2009/02/04 11:40 (external edit)

    Home  |   About Us  |   Contact Us  |   Statistics
Recent changes RSS feed Creative Commons License Donate Powered by PHP Valid XHTML 1.0 Valid CSS Driven by DokuWiki