About ecellJ

The software system ecellJ is a package for manipulating rule files for the ecell system which is used to simulate biological reaction networks. ecellJ  was created by Jörg R. Weimar during a reserach stay at the Institute for Advanced Biosciences, Keio University, Japan.
The software is copyright © Jörg Weimar, 2003.

This is version 0.4 of ecellJ.

Current capabilities include:

Requirements, Starting

ecellJ is distributed as a single jar-file and requires java 2 (version at least java 1.2).
Start ecellJ by double-clicking the jar-file (windows) or by typing
java -jar ecellJ.jar
You will see a small window with a menu.
  Changes in Version 0.2.1: - Added menu item to produce a simple textual list of reactions. All reactions are printed as reversible, since the information on reversibility is not available in ecell rule files.
- Added simple SBML export. Only a few rate laws are currently exported if standard reactors are used.

  Changes in Version 0.3 ( March 25, 2003) - Added simple SBML import. Needs some more work,as the rates are not imported, the parameters are not shown, etc.
- fixed errors in SBML export
  Changes in Version 0.3.1 ( March 28, 2003)
- Fixed some error in importing spread sheet files (.csv).
- improved SBML import: effectors are now identified as all those substances that enter the rate law but are neither substrates nor products. Still missing: identify catalysts as those effectors for which the rate is proportional to the concentration. This requires the full parse tree of the expression and some manipulations on trees.
- added icon to HTML files.