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