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
Load and Save SBML
Translate to Jarnac, Matlab, etc
Supports time dependent simulation and steady state
Stoichiometric Analysis via Metatool
Reactions, Compartments, Regulation, Alias Nodes, boundary and floating nodes
Graphing of data, many options
Load external data onto simulated data
Annotate model, reaction, nodes and compartment with HTML
Built-in or free format kinetic rate laws
Rate law explore tool
Molecules designer for visualization
Most if not all visual attributes can be modified
Use of sliders for real-time interaction simulation
Graphing or tabular output (eg export to Excel)
Autolayout of networks
Generate publishing quality graphs in PDF
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 Tutorial Videos.
How to Change the Simulator in JDesigner
List of supported operators and functions for writing rate laws and assignment rules:
+, -, /, *, ^ (power), (, )
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