Software support for SBGN maps: SBGN-ML and LibSBGN

Creators: van Iersel, Martijn P.; Villéger, Alice C.; Czauderna, Tobias; Boyd, Sarah E.; Bergmann, Frank T.; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I.; Mi, Huaiyu; Moodie, Stuart L.; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

Abstract

Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net.

Additional Information

© 2012 The Author(s). Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Advance Access publication May 10, 2012. The authors thank their individual sources of funding. Authors are grateful for useful feedback from the Path2Models project. Funding: This work was in part supported by the Biotechnology and Biological Sciences Research Council (BBSRC); the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research; BioPreDyn which is a grant within the Seventh Framework Programme of the EU, the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research; and the German Ministry of Education and Research (BMBF). Conflict of Interest: none declared.

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