SBMLeditor

The need to build a tool to facilitate the quick creation and edition of SBML (Hucka et al., 2003) files has been growing with the number of users and the increased complexity of the Level 2 (and the future Level 3). SBMLeditor tries to answer this need by provided a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. SBMLeditor provides the ability to use the annotation framework, based on RDF and dublin core elements and now part of SBML since SBML Level 2 Version 2. Some functions provided by libSBML are available if the library is setup properly on the system.

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 instructions

SBMLeditor is distributed under the General Public Licence.

Latest stable version is 1.3.4 (16/11/2009)

You can have a look at the ChangeLog to see what's new.

• You will need the Java JRE 1.5 or higher to install and run the SBMLeditor. You can download it from the Java web site
• libSBML-4.0.0 is included for some platforms: Windows 32bit, Linux 32bit and 64bit, MacOSX i386 and ppc.
• download the Windows installer
• download the GNU/Linux-MacOSX installer
• download the tar.gz archive. If you have some problems with the automatic installers, you can download this version. You just have to unpack it and it should be ready to use if java is set correctly on your system. The only reported problem is that you cannot launch the installer directly from the download page of your browser, you have to go to the folder where you saved it and launch it from there.

Screenshots:

• MathML editor
• MathML as free text
• RDF annotations

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).

For Windows, libSBML is included with the SBMLeditor package, so no need to change anything. There might be a conflict if you have an older libSBML installed under windows system files. In that case, you will have to choose one or the other libSBML version and configure the SBMLeditor accordingly, either by deleting/moving the dll in the SBMLeditor folder, either by deleting/moving the libSBML dll under the windows system files. An other option in that last case, is to uninstall libSBML and install it again but selecting the custom installation and do not select the check box "Copy libraries to systems directories".

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 :

chmod +x SBMLeditor-1.3.4-20091116-install.sh

To allow the file to be executed and then, type :

./SBMLeditor-1.3.4-20091116-install.sh

to run the setup.

Getting Help and Support

The 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.
You can download it there : SBMLeditor Manual

Until we have a tracker dedicated to SBMLeditor, please send any help requests or bug reports to :

Please, use the string "[SBMLeditor]" in the title of your mail.

Getting the source code

The sources are included in the SBMLeditor packages but you can also get them directly from the SBML sourceforge project :

svn co https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/sbmleditor

To Browse the source code :

http://sbml.svn.sourceforge.net/viewvc/sbml/trunk/sbmleditor/

How to cite SBMLeditor