title: The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
authors.affiliation: Department of Pharmacology M.Aiazzi Mancini, University of Firenze, 50139 Firenze, Italy.
authors.forename: Luca
authors.initials: L
authors.lastname: Beltrame
authors.forename: Enrica
authors.initials: E
authors.lastname: Calura
authors.forename: Razvan R
authors.initials: RR
authors.lastname: Popovici
authors.forename: Lisa
authors.initials: L
authors.lastname: Rizzetto
authors.forename: Damariz Rivero
authors.initials: DR
authors.lastname: Guedez
authors.forename: Michele
authors.initials: M
authors.lastname: Donato
authors.forename: Chiara
authors.initials: C
authors.lastname: Romualdi
authors.forename: Sorin
authors.initials: S
authors.lastname: Draghici
authors.forename: Duccio
authors.initials: D
authors.lastname: Cavalieri
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software