Software - sbgn.org This page summarizes what we know about software support for SBGN languages. This knowledge comes from a variety of sources, and is necessarily incomplete. If your software is not listed below, or if you know of another effort, please post a message to sbgn-discuss@sbgn.org. Software tool assisting in supporting SBGN The implementation of SBGN support in software tools may be facilitated by the use of an XML exchange format: SBGN-ML. SBGN-ML can be processed and generated by a standard library: LibSBGN. Discussions around SBGN-ML and LibSBGN take place on sbgn-libsbgn-discuss One can compare the rendering of SBGN-ML by the different software using the LibSBGN Render Comparison site or Frank Bergmann's Render Comparison site. Software providing support for SBGN The following is a list of software packages known to provide (or have started to develop) support for SBGN notations. Contact: duccio . cavalieri @ unifi . it
Bioinformatics Software Interoperability (BSI) SIG The explosion of genomic data over the past decade, accelerated by the widespread adoption of next-generation sequencing, has been matched by a proliferation of software tools to analyze, visualize, and manage it. This wealth of individual tools calls for environments to support their interoperation along with multi-tool analytic workflows, transfer of data between tools, recording of analytic provenance, and facilitation of reproducible research. These features are crucial to address the heightened demand for accessibility and reproducibility now being placed on genomic researchers and data production centers. This SIG will explore approaches to interoperable bioinformatics software. It will include presentations on a number of well-established bioinformatics interoperability environments and demonstrate how they can support the research of bench biologists. Date Friday, July 13, 8:30 a.m. – 6:30 p.m. Sessions More Information Please contact bsi-sig-2012@broadinstitute.org
Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization Welcome to a Little Book of R for Bioinformatics! — Bioinformatics 0.1 documentation By Avril Coghlan, Wellcome Trust Sanger Institute, Cambridge, U.K. Email: alc@sanger.ac.uk This is a simple introduction to bioinformatics, with a focus on genome analysis, using the R statistics software. To encourage research into neglected tropical diseases such as leprosy, Chagas disease, trachoma, schistosomiasis etc., most of the examples in this booklet are for analysis of the genomes of the organisms that cause these diseases. There is a pdf version of this booklet available at: If you like this booklet, you may also like to check out my booklet on using R for biomedical statistics, and my booklet on using R for time series analysis,