spacer
spacer

SBMLeditor

The Systems Biology Markup Language (SBML) is a free and open interchange format for encoding computational models of biological processes. SBML aims to be a systems to systems format, and users are not expected to write SBML files manually.

SBMLeditor is a simple, low-level editor for SBML files. It allows you to manipulate SBML elements in a controlled way, whilst maintaining the validity of the final file.

SBMLeditor also allows you to create and modify annotations, as defined in the SBML specifications.


Screenshots:


MathML editor example MathML free text editor example Annotation example

Download / Install


Latest version is 2.0-b1 (29/06/2012)

SBMLeditor is distributed under the General Public Licence.


What's new

  • support for SBML Level 3 Version 1 core has been added
  • JSBML is used to read and write the SBML files.
  • libSBML is used remotely to validate the SBML models.
  • you can customized the colors used in the math editor

Installation instructions

Once you complete the download, you need to uncompress the archive. Then, you just have to execute runSBMLeditor.sh (under Windows, use runSBMLeditor.bat) to start the editor. Some samples data are available under the data directory, you will find all the published SBML models from the BioModels Database (Release 22).


Getting help and support

A user manual is being written. You can already download the unfinished manual, where you will be able to find useful information to start using 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.

Development

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

You can also directly browse the source code on sourceforge.


Implementation details

SBMLeditor is written in Java using JCompneur, a library developed by Marco Donizelli that provides an interface 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 editing and validating 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. SBMLeditor also checks before any element deletion that it would not break a reference in the rest of the document.


How to cite SBMLeditor


Rodriguez N, Donizelli M, Le Novère N (2007)
SBMLeditor: 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]
 
                                                                                                                   
 
spacer
spacer