From libsbgn

Please note, this is an old version of the LibSBGN wiki. The current version can be found here.

Contents 1 About the LibSBGN Project 1.1 Download 1.2 The SBGN-ML format 1.3 The LibSBGN library 1.4 Current status 2 Documentation 2.1 General information 2.2 ... for tool developers 2.3 ... for LibSBGN developers 3 The LibSBGN Development Process 4 Software Support 5 Example Files 6 MediaWiki Usage

About the LibSBGN Project

The main goal of the LibSBGN Project is to provide a standard electronic implementation for the Systems Biology Graphical Notation (SBGN).

Download

Please also see the Release Notes

• libsbgn-milestone2.zip
• libsbgn-milestone2.tar.gz

The SBGN-ML format

SBGN-ML is an XML-based file format dedicated to the description of SBGN maps.

For more information, refer to the page dedicated to this Exchange Format.

The LibSBGN library

LibSBGN is a library that deals with SBGN maps. It features:

• Reading / writing the SBGN-ML file format
• Validation (of semantical and syntactical correctness) See ValidationEntryPage
• Conversion to other formats such as SBML and BioPAX
• Support for at least Java and C++

Current status

LibSBGN and SBGN-ML are still in development. See SBGN-ML_Roadmap

Documentation

General information

• LibSBGN presentation at COMBINE 2010
• LibSBGN poster presented at COMBINE 2010 and ISCB 2010
• LibSBGN tutorial presented at HARMONY 2011
• LibSBGN status update presented at COMBINE 2011

... for tool developers

• Developer tutorial This is a tutorial for developers who want to add LibSBGN support to their tool.
• Java API Docs

... for LibSBGN developers

• Benchmark

The LibSBGN Development Process

We're currently defining the Exchange Format. To see what was discussed in the past, see OnlineMeetings#Past Meetings and the mailing list hosted in the SBGN project

We hold semi-monthly online meetings. For information about past and future meetings, see: OnlineMeetings. For the latest information about upcoming meetings, please contact the mailing list. We also have live discussions bi-annually at COMBINE and HARMONY:

• COMBINE 2012
• HARMONY 2011
• HARMONY 2012

Implementation plan: SBGN-ML_Roadmap

The development of LibSBGN is articulated around a number of online tools (mostly hosted on SourceForge):

• the SVN repository
• the bug tracker (See also: Bug tracker FAQ)
• the mailing list

Software Support

LibSBGN is being adopted by a number of tools. For an up-to-date list, see ClientTools. To see how these tools render SBGN-ML files, see our render comparison page.

Example Files

Some example files created with LibSBGN can be found here: SBGN-ML Example Files.

MediaWiki Usage

Consult the User's Guide for information on using the wiki software.