TY - JOUR
AU - Cavalieri, Duccio
AB - Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions.Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists.Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.Contact: duccio.cavalieri@unifi.it; sorin@wayne.eduSupplementary information: Supplementary data are available at Bioinformatics online.
TI - The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways
JF - Bioinformatics
DO - 10.1093/bioinformatics/btr339
DA - 2011-06-07
UR - https://www.deepdyve.com/lp/pubmed-central/the-biological-connection-markup-language-a-sbgn-compliant-format-for-sCxLJBo0KQ
SP - 2127
EP - 2133
VL - 27
IS - 15
DP - DeepDyve
ER -