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 files

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. ecellJ can read these files directly. The format is described in the documentation for e-cell.

A template for a spread sheet file is template.txt.

ER files

ER files are descriptions of the rule in a structured format. A simple ER file is given here. It consists of one section for each

system
substance
reactor

Each section has the same basic structure:

type name(/PATH:COMPONENT,"A descriptive text")
{
ArgumentName1 ArgumentValue1;
ArgumentName2 ArgumentValue2;
}

where

type is one of system,substance, reactor,
name is

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

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 tool
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 File->Save dialog.

SBML files

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.