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 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.

Arcadia: a visualization tool for metabolic pathways.

SUMMARY: Arcadia translates text-based descriptions of biological networks (SBML files) into standardized diagrams (SBGN PD maps). Users can view the same model from different perspectives and easily alter the layout to emulate traditional textbook representations. AVAILABILITY AND IMPLEMENTATION: Arcadia is written in C++. The source code is available (along with Mac OS and Windows binaries) under the GPL from http://arcadiapathways.sourceforge.net/.