Computational Systems Biology
Sauro Lab
University of Washington
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Software Downloads:

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

JDesigner: A Biochemical Network Layout Tool

Download
SBW

Documentation
JDesigner Tutorials

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

Screen Shots

Summary of Features

  1. Load and Save SBML
  2. Translate to Jarnac, Matlab, etc
  3. Supports time dependent simulation and steady state
  4. Stoichiometric Analysis via Metatool
  5. Reactions, Compartments, Regulation, Alias Nodes, boundary and floating nodes
  6. Graphing of data, many options
  7. Load external data onto simulated data
  8. Annotate model, reaction, nodes and compartment with HTML notes
  9. Built-in or free format kinetic rate laws
  10. Rate law explore tool
  11. Molecules designer for visualization
  12. Most if not all visual attributes can be modified
  13. Use of sliders for real-time interaction simulation
  14. Graphing or tabular output (eg export to Excel)
  15. Autolayout of networks
  16. Generate publishing quality graphs in PDF

Videos

Installation

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.

Documentation & Help

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

 
sysbio/jdesigner.txt · Last modified: 2011/01/16 17:26 (external edit)
 

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