ecellJ File Reading Capabilities
The software system ecellJ can read e-cell rule files in
any of the three formats used by e-cell1 and e-cell2:
Spread sheet rule files are created for example by Openoffice
or any other spread-sheet program. They must be saved in a plain text
format, using tabs as separators between the columns.
In ecell1 these files are converted to ER-format by the tool ss2er.
can read these files directly. The format is described in the documentation
A template for a spread sheet file is template.txt.
ER files are descriptions of the rule in a structured format. A
ER file is given here. It consists of one section for each
Each section has the same basic structure:
type name(/PATH:COMPONENT,"A descriptive text")
type is one of system,substance, reactor,
a string for systems,
Substance for Substances, and
the reactor type (name of the .rd file) for reactors.
/PATH:COMPONENT describes the path of the component,
and the arguments are given inside the braces.
ERI files are written in an internal tab-separated format which ecell-1
can read. In ecell-1, these files are produced from er files using the
er2eri file.er >file.eri
while ecellJ can write eri files directly. For writing
eri files, simply specify a file with the extension .eri in the
A first attempt has been made to export SBML files. Only some rate laws are exported.
Use file extension ".xml" or ".sbml" to save files in this format.