JDesigner: A Biochemical Network Layout Tool

JDesigner is a Win32 application which allows one to draw a biochemical network and export the network in the form of SBML. The Designer has an SBW interface that allows it to be called from other SBW compliant modules, for example Python. In addition, JDesigner has the ability to use Jarnac or roadRunner as a simulation server (via SBW) thus allowing models to be run from within JDesigner. In this mode JDesigner is both a network design tool and simulator. Full binaries and source code is available in the download.

JDesigner is an Open Source Project distributed under the BSD license.

Development of JDesigner was initiated by Future Skill Software in 1997 but was subsequently supported from 2000 by the Kitano ERATO project at Caltech and more recently by an NIH grant GM081070

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

JDesigner is fully supported on Windows, but is not supported on Mac OS X and Linux.

JDesigner Quickstart

JDesigner Tutorials

JDesigner Tutorial Videos.

How to Change the Simulator in JDesigner

JDesigner FAQ

List of supported operators and functions for writing rate laws and assignment rules:

Operators

+, -, /, *, ^ (power), (, )

Functions

sin, cos, tan, exp, log (base 10), ln (base e), sqr (x2), sqrt, fact (factorial), arcsin, arccos, arctan, sinh, cosh, tanh, arcsinh, arccosh, arctanh, abs, pow, piecewise, gt

Also included is the implicit variable 'time'.

piecewise take three arguments

gt takes two arguments

— Frank Bergmann 2006/08/31 11:38