ANNOUNCE: Update to Jarnac, metabolic simulation software

Herbert M Sauro HSauro at fssc.demon.co.uk
Mon Jun 26 18:29:16 EST 2000

Jarnac: Interactive Metabolic Simulation Tool for Windows 95/98/NT

What is Jarnac:

Jarnac can be used as a general purpose language for performing arithmetic
operations, including matrix and vector arithmetic, numerical
differentiation and integration, and a function or data grapher. The real
usefulness of Jarnac however is its ability to manipulate, analyse and
simulate metabolic networks. There is built-in computational support for
dynamic simulation (using LSODA integrator), steady state analysis using the
NLEQ solver, simple stability analysis, continuation, matrix arithmetic,
Metabolic Control Analysis (All steady state control coefficients and
elasticities) and Metabolic Structural Analysis (Null space, elementary
modes (via MetaTool) conservation relation analysis etc). Jarnac hosts a
full programming language including many different data types, control
loops, user defined functions, modules etc.

And it's entirely free, becoming open-source some time this summer and if
all goes to plan, a Linux release at the end of the year.

A new version of Jarnac 1.16 is now available at


Changes include (see history for details)

1. Minor bug fix to user function calling (see history for details)
2. Exception handling implemented
3. Added SizeOf (x), get number of bytes occupied by x
4. Added Dim (v|m), get dimension of matrix/vector as a list
5. Added Mark method to graph object
6. File History added to editor
7. New methods for graph object, 'hide' and 'show'
8. New constructors added to graph object
9. New method, 'join' added to graph object
10. New property, 'axes', to set all axes limits in one call, cf. xmax, xmin
11. New key word, extern added to language to allow access to external
variables in user functions
12. New key word, break added to allow control to exit from while/repeat/for
13. More examples
14. Updated documentation
15. Updated MetaTool executable (fixes small problem)
16. Steady state continuation algorithm for following stable and unstable
steady states.

Herbert Sauro
June 2000

Herbert Sauro
// Remove the space between f and s before using email address
email: HSauro at f ssc.demon.co.uk
"He who cannot draw on 3000 years is living from hand to mouth" Goethe
"Ah, but a man's reach should exceed his grasp, or what's a heaven for?"
R Browning.

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