title: SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.
abstract: BACKGROUND
  Studies of cellular signaling indicate that signal transduction pathways combine to form large networks of interactions. Viewing protein-protein and ligand-protein interactions as graphs (networks), where biomolecules are represented as nodes and their interactions are represented as links, is a promising approach for integrating experimental results from different sources to achieve a systematic understanding of the molecular mechanisms driving cell phenotype. The emergence of large-scale signaling networks provides an opportunity for topological statistical analysis while visualization of such networks represents a challenge.
  
  
  RESULTS
  SNAVI is Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names.
  
  
  CONCLUSIONS
  SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software. The installation may be downloaded from: http://snavi.googlecode.com. The source code can be accessed from: http://snavi.googlecode.com/svn/trunk.
authors.affiliation: Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA. avi.maayan@mssm.edu
authors.forename: Avi
authors.initials: A
authors.lastname: Ma'ayan
authors.forename: Sherry L
authors.initials: SL
authors.lastname: Jenkins
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Webb
authors.forename: Seth I
authors.initials: SI
authors.lastname: Berger
authors.forename: Sudarshan P
authors.initials: SP
authors.lastname: Purushothaman
authors.forename: Noura S
authors.initials: NS
authors.lastname: Abul-Husn
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Posner
authors.forename: Tony
authors.initials: T
authors.lastname: Flores
authors.forename: Ravi
authors.initials: R
authors.lastname: Iyengar
mesh_terms: D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology; D014584:User-Computer Interface