Bibliosphere Analysis Kit

BiblioSphere offers a unique combination of literature-mining and pathway analysis for molecular biologists interested in gene regulation and biological networks.
BiblioSphere Pathway Edition uses a comprehensive database of individually modeled relationships between genes, proteins, complexes, cells and tissues together with up-to-date text mining techniques for automated knowledge extraction to allow you to link your data to biological networks in different biological contexts.

Use BiblioSphere to

• extend biological networks beyond canonical pathway information (regulatory & metabolic)
• merge your high throughput results with biological knowledge and sequence based analyses
• perform context-sensitive regulatory pathway analysis
• generate experiment-specific pathway variants
• link pathways to disease mechanisms & genes
• do advanced experimental design

New in 5.11:

What is new in this release:

New and Enhanced Data Sources

• Genomatix Expert Curated Gene-Gene Relations:
  Genomatix has integrated its proprietary knowledge-base of expert curated data on gene regulation into BiblioSphere. This unique data source adds the semantics of gene-gene relationships to the dynamically generated BiblioSphere gene networks, providing information like "Gene A activates transcription of gene B" or "Gene A physically interacts with gene B".
  
• Signal Transduction Pathways:
  Portions of Gene Ontology relevant to signal transduction as well as data compiled from literature have been combined to enable the identification of canonical pathways linked to the focused network.
  
• Metabolic Pathway Associations:
  Metabolic pathway associations have been integrated to allow the identification of metabolic events relevant to your set of genes.
  

New or Enhanced Views

• Pathway View with expert curated gene-gene relationships
  Gene groups are compiled into easily comprehensible dynamic network graphs combining hand curated gene-gene relationships with data derived from automated knowledge extraction. Networks can be customized by filters and focused in a gene centered way to perform shortest path analysis.
  
• Cellular Localization View
  Based on GO Annotations genes are assigned to their subcellular location and visualized as a diagrammed cell layout, allowing you to identify subcellular regions and compartments relevant to your gene set.
  

Other new features

• Project Management: Manage your analyses by organizing them into project folders. Quickly access previous results with a few mouse clicks or add new searches to existing projects.
  

New in 5.11:

• Various small enhancements and bugfixes

Requirements:

• Mac OS X 10.2 or higher
• Java 1.4.1 (update 1 is recommended)
• connection to the internet
• a Genomatix evaluation account (free of charge)