Software support for SBGN maps: SBGN-ML and LibSBGN.

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TitleSoftware support for SBGN maps: SBGN-ML and LibSBGN.
Publication TypeJournal Article
Year of Publication2012
Authorsvan Iersel, MP, Villéger, AC, Czauderna, T, Boyd, SE, Bergmann, FT, Luna, A, Demir, E, Sorokin, A, Dogrusoz, U, Matsuoka, Y, Funahashi, A, Aladjem, MI, Mi, H, Moodie, SL, Kitano, H, Le Novère, N, Schreiber, F
JournalBioinformatics
Volume28
Issue15
Pagination2016-21
Date Published2012 Aug 1
ISSN1367-4811
KeywordsComputational Biology, Programming Languages, Software, Systems Biology
Abstract

<p><b>MOTIVATION: </b>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.</p><p><b>AVAILABILITY AND IMPLEMENTATION: </b>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.</p><p><b>CONTACT: </b>sbgn-libsbgn@lists.sourceforge.net.</p>

DOI10.1093/bioinformatics/bts270
Alternate JournalBioinformatics
PubMed ID22581176
PubMed Central IDPMC3400951
Grant List / / Biotechnology and Biological Sciences Research Council / United Kingdom
/ / Intramural NIH HHS / United States