Abstract
AbstractLibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.For more information:http://libsbgn.sourceforge.net
Highlights
Context & MoHvaHon WHY LIBSBGN?Growing SBGN soKware support Arcadia Athena BiNoM BioModels Database BioPAX BioUML ByoDyn CellDesigner Dunnart Edinburgh Pathway Editor JWS Online Mayday Netbuilder (Apostrophe) PANTHER PathwayLab Reactome Vanted VISIBIOweb ... 19 toolsCf. h\p://sbgn.org/SBGN_SoKwareMulHple electronic representaHons Model (= network + biological semanHcs ) + layout + rendering– SBML + layout and rendering extension– Celldesigner SBML– BioPAX + layout extension
Arcs refer to glyph or glyph ports
Just ask any of the project members to get added h\p://libsbgn.sourceforge.net
Summary
JWS Online Mayday Netbuilder (Apostrophe) PANTHER PathwayLab Reactome Vanted VISIBIOweb ... – But features they need (e.g. validaHon, layout) may be sca\ered across different pieces of soKware!. – The same set of core features (e.g. conversion to and from usual formats) gets implemented mulHple Hmes. – facilitate development of SBGN compliant tools – increase interoperability between these tools Electronic implementaHon of SBGN – Exchange format for all SBGN maps: SBGN-‐ML. Object model and API, in Java and C++ key features: conversion, validaHon and layout
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