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Software support for SBGN maps: SBGN-ML and LibSBGN
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...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400951/ https://www.ncbi.nlm.nih.gov/pubmed/22581176 http://dx.doi.org/10.1093/bioinformatics/bts270 |
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author | 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 |
author_facet | 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 |
author_sort | van Iersel, Martijn P. |
collection | PubMed |
description | 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. Contact: sbgn-libsbgn@lists.sourceforge.net |
format | Online Article Text |
id | pubmed-3400951 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-34009512012-07-20 Software support for SBGN maps: SBGN-ML and LibSBGN 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 Bioinformatics Original Papers 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. Contact: sbgn-libsbgn@lists.sourceforge.net Oxford University Press 2012-08-01 2012-05-10 /pmc/articles/PMC3400951/ /pubmed/22581176 http://dx.doi.org/10.1093/bioinformatics/bts270 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 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. |
spellingShingle | Original Papers 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 Software support for SBGN maps: SBGN-ML and LibSBGN |
title | Software support for SBGN maps: SBGN-ML and LibSBGN |
title_full | Software support for SBGN maps: SBGN-ML and LibSBGN |
title_fullStr | Software support for SBGN maps: SBGN-ML and LibSBGN |
title_full_unstemmed | Software support for SBGN maps: SBGN-ML and LibSBGN |
title_short | Software support for SBGN maps: SBGN-ML and LibSBGN |
title_sort | software support for sbgn maps: sbgn-ml and libsbgn |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400951/ https://www.ncbi.nlm.nih.gov/pubmed/22581176 http://dx.doi.org/10.1093/bioinformatics/bts270 |
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