Software

BiologicalNetworks 1.9 (current)

10 Dec 2007

New features added:

• Finding associations among pathways, expression patterns and functional annotations
  • Visualizing, filtering and exploring associations
  • Finding biological significance of associations
• Co-occurence discovery:
  • Discovering significant annotations enriched in a gene list and microarray experiment
  • Discovering significant annotations enriched in a microarray experiment and curated pathways
• Import/export
  • Improved curated pathways import
  • Improved SBML support
• Clustering nodes in network based on GO annotations
• Search for genes and proteins in curated pathways
• Tested on Java 5 and 6

Download v1.9

BiologicalNetworks 1.5

18 May 2007

New features added:

• SBML support
• Save complete BNProject
• Open model from archive file
• New Visual Mapper:
  • Node visual properties customization
    • Set node color, border color
    • Set tumbnail
  • Node visual properties customization
    • Set color, width and stroke for individual edge
    • Set color, width and stroke for all edge of specified type
• Works on Windows and Mac OS X
• Tested on Java 5

BiologicalNetworks 1.0

04 Apr 2006

• Build pathways
• Expand pathway
• Use filtering
• Find shortest path between two genes or all shortest paths covering group of genes
• Find only direct interactions
• Find common targets or find common regulators
• Find intersections with known curated pathways
• Explore pathways
• Move, drag and drop biological components on the workspace
• Cut, Copy, Paste and Delete biological components
• Different layout algorithms
• ZoomIn/ZoomOut/ZoomToFit
• Variety of preloaded curated common pathways
• Supported file formats: SIF, GML, XML, tab delimited
• Network Analysis and Statistics
• Network statistics
• Finding cycles
• Pathway Homology
• Node and Connector Tables
• Microarray Gene Expression Data
• Import microarray gene expression data sets
• Filter, Normalize, make Data transformations
• Different clustering methods
• Derive microarray expression correlation networks
• Overlay expression data onto an open network
• Sort and search over your expression data