BiologicalNetworks BiologicalNetworks

Software

BiologicalNetworks v. 2.0 betta

01 April 2010

  • Several additional functions and search options introduced into BuildPathwayWizard for extensive network navigation.

  • In addition to GeneOntology annotations multiple additional ontology annotations were added:
    • Diseases
    • Cell Types
    • Tissues
    • Mammal Phenotypes
    • Human Anatomy
    • Mouse Anatomy
    • KEGG Pathways
    • Chemicals

  • MetaNodes functionality extended with representation of Curated Pathways as MetaNodes in MetaNetworks

  • JMol viewer for 3D protein structure visualization added

  • Network visualization and navigation extended:
    • Layouts
    • Scaling
    • Editing

  • Sequence Analysis Module extended:
    • GenBank genomic sequences available
    • Gene regulatory regions integrated from over a 100 public data sources on gene regulation available
    • Transcription factors mappings to respective regulatory regions available

  • Many bugs fixes

07 January 2010

  • Sequence Analysis environment integrated into the main Window of BiologicalNetworks.

  • All the functionality of the older version 1.9 is carried over to the new platform.

  • Tested on Java 5 and 6, Windows and Mac OS X

  • Back end database now reaches 2 TB of the data integrated from over 100 public data sources.

  • Many bugs fixes

BiologicalNetworks v. 2.0 alpha

01 May 2009

New features added:

  • New NetBeans professional platform from SUN Microsystems. The NetBeans platform is acknowledged as a standard by hundreds of thousands of developers of project oriented systems around the world, developing applications of all sizes and complexity:
    • Powerful and robust base
    • Modular architecture
    • Robustness to system fails and big data loads
    • Rapid development of custom modules (analytical, graphical, data processing)
    • Integration of new resources into the framework with minimal effort
    • Enhanced support for software development of modules on Java, C/C++, PHP, Ajax and JavaScript, Groovy and Grails, Ruby and Ruby on Rails as well as support for web frameworks (Hibernate, Spring, JSF, JPA), the GlassFish application server, and databases

  • Intuitive and customizable Visual Interface
    • Dragging and dropping visual components from a palette onto a canvas.
    • Floating windows

  • Research and analysis enhancements
    • New Demo Page representing Driving Projects and Example Research Modules
    • Advanced tree structure of every project which contains project with the all the associated data (e.g. microarray experiments, 3d images, etc.)
    • Advanced Curated Data Panel, containing curated data associated with every Research Module: Networks/Pathways - KEGG, BioNets Pathways, Microarrays- NCBI-GEO Microarrays, Genomic Sequences - NCBI, RefSeq

Download v2.0

BiologicalNetworks v. 1.9

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-occurrence 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 v. 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 thumbnail
    • 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 v. 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