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

Bioinformatics
Martijn P van IerselFalk Schreiber

Abstract

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. 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. sbgn-libsbgn@lists.sourceforge.net.

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Citations

May 3, 2013·Molecular BioSystems·Magdalena RotherMarcus Krantz
Oct 16, 2012·Briefings in Bioinformatics·Santo Motta, Francesco Pappalardo
Jan 18, 2013·BMC Bioinformatics·Emanuel GonçalvesJulio Saez-Rodriguez
Nov 13, 2012·BMC Systems Biology·Hendrik RohnFalk Schreiber
Nov 5, 2013·BMC Systems Biology·Finja BüchelNicolas Le Novère
Sep 27, 2013·PLoS Computational Biology·Emek DemirChris Sander
Jun 18, 2014·BMC Systems Biology·Hsueh-Chien ChengMartin Meier-Schellersheim
Jan 3, 2016·Journal of Biotechnology·Rafael S CostaSusana Vinga
Dec 17, 2014·BMC Bioinformatics·Frank T BergmannNicolas Le Novère
Dec 31, 2014·BMC Bioinformatics·Alberto NoronhaMiguel Rocha
Sep 13, 2015·Bioinformatics·Begum Genc, Ugur Dogrusoz
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Jun 17, 2015·Bioinformatics·Nicolas RodriguezAndreas Dräger
Apr 19, 2015·BMC Systems Biology·Anna Zhukova, David J Sherman
Apr 12, 2013·Bioinformatics·Falko KrauseThomas Handorf
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Aug 28, 2015·PLoS Computational Biology·Zachary A KingBernhard O Palsson
Jun 17, 2016·BMC Systems Biology·Adrien RougnyLoïc Paulevé
Dec 31, 2016·ACS Synthetic Biology·Zach ZundelChris J Myers
Mar 30, 2018·Journal of Integrative Bioinformatics·Falk SchreiberDagmar Waltemath
Aug 29, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Haitham ElmarakebyLenwood S Heath
Jun 7, 2018·NPJ Systems Biology and Applications·Alexander MazeinCharles Auffray
Dec 7, 2018·Bioinformatics·Andrew PartonSteven Watterson
Jan 7, 2020·Bioinformatics·Irina BalaurAndrei Zinovyev
Jul 1, 2020·Journal of Integrative Bioinformatics·Dagmar WaltemathChris J Myers
Jul 6, 2019·Briefings in Bioinformatics·David HokszaReinhard Schneider
Aug 28, 2020·Molecular Systems Biology·Sarah M KeatingUNKNOWN SBML Level 3 Community members
Oct 7, 2015·Briefings in Bioinformatics·Andrew PartonSteven Watterson
Mar 25, 2016·Current Protocols in Bioinformatics·David S Wishart
Dec 7, 2016·BMC Bioinformatics·Vasundra TouréCharles Auffray
Jun 15, 2019·Journal of Integrative Bioinformatics·Dimitar GarkovFalk Schreiber
May 10, 2019·Bioinformatics·Adrien Rougny
Oct 28, 2019·Nucleic Acids Research·Igor RodchenkovChris Sander
Apr 28, 2018·BMC Systems Biology·Frank KramerTanja Zeller

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Software Mentioned

ChIBE
Sourceforge
PathVisio
Schematron Validation Report Language ( SVRL
ML
ED
Java
PaxTools
SBGN
SBML

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