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:
Read and write Ecell rule files (.er)
Read and write E-cell internal rule files (.eri)
Read E-cell spread sheet files (.txt or .csv).
Read and write SBML files with limited support for kinetic laws (.xml or .sbml).
Display the rule in a structured GUI.
Calculate the stoichiometric matrix.
Calculate the conservation laws.
Generate a super-reactor from slave-reactors for use with the hybrid static/dynamic
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
- added icon to HTML files.