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SBMLeditor SBMLeditor is written in JAVA using JCompneur, a library developed by Marco Donizelli who provide interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the edition and validation of the document. For example, in SBMLeditor, all attributes that require a reference to another group of tags are represented as a list instead of free text. This, in turn, speeds up the creation of the document and avoid any typing error. We also check before any element deletion that it would not break a reference in the rest of the document. Download/Install instructionsSBMLeditor is distributed under the General
Public Licence.
TODO for next versions. Screenshots: Once you complete the installation you just have to type ./runSBMLeditor.sh (Under Windows, use the shortcut on your desktop or runSBMLeditor.bat) on the directory where you installed the editor. Some samples data are available under the data directory, you will found all the published SBML models from the BioModels Database For Unix/Mac, If you have a version of libSBML already installed and you want to use it, you might have to
edit the run script to enter the location of your
libSBML installation. You have to specify the location
of the jar file into the CLASSPATH and if necessary the
location of the libraries files into the LD_LIBRARY_PATH
(for linux only, for more details and for other systems than
linux, see the libSBML
Java documentation). You can use the latest versions of libSBML. For the latest OS, like the MacOSX 64bits or Window 7 64bits, you will need to install your own version of libSBML as the provided libSBML will not work. You can download libSBML from their sourceforge project. Then it should be working with small changes in the startup script. Below is an example for OSX :
First replace the LIBSBML_HOME declaration to be /usr/local (changed that if you installed it in a different path) :
if [ "$OS" = "Darwin" ] ; then
# LIBSBML_HOME=./lib/libsbml-libxml2-4.0.0.macosx
LIBSBML_HOME=/usr/local
DYLD_LIBRARY_PATH=${LIBSBML_HOME}/lib
export DYLD_LIBRARY_PATH
fi
And then, you need to update the SBML_CLASSPATH line :
SBML_CLASSPATH=${LIBSBML_HOME}/share/java/libsbmlj.jar:./lib/libsbml-4.0.0-utils.jar
The interfaces I used did not changed since libsbml-4.0.0 that's why we can use the libsbml-4.0.0-utils.jar jar file.
WARNING : the installer is not working if you try to
open it directly from the firefox download manager (or other browser) on Linux or Mac.
You should go to the folder where you saved the installer and type :
Getting Help and SupportThe manual is not written yet. But as many people requested some documentation, we provide you an unfinished manual
where you should be able to find some useful informations to start using SBMLeditor.
Until we have a tracker dedicated to SBMLeditor, please send any help requests or bug reports to : biomodels-net-support at lists.sourceforge.net Please, use the string "[SBMLeditor]" in the title of your mail. Getting the source codeThe sources are included in the SBMLeditor packages but you can also get them directly from
the SBML sourceforge project :
How to cite SBMLeditorSBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML).
BMC Bioinformatics, 8:79
[OpenAccess] abstract full-text HTML full-text PDF [PMID: 17341299] [doi:10.1186/1471-2105-8-79]
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