Download BioNetwork bench 1.6.4 for free!
BioNetwork bench is a flexible interactive database querying system for storing and manipulating gene expression data and genetic networks, constructing networks from expression data, iteratively querying multiple networks and expression datasets, and merging and re-using the results obtained.
The plugin provides multiple capabilities for users of different types
- All users
- Manipulating (loading, saving, deleting) private and public data (gene expression data, networks)
- Constructing correlation networks
- Querying multiple private and public datasets to find
- Coexpressed genes
- Nodes with certain annotations (stored in the database or fetched from Gene Ontology)
- Links with certain annotations
- Sharing private networks and datasets with other users
- Experts
- Populating the database
- Administrators
- Installing and managing the database
- Managing user accounts
Our goal was to build a software system that would allow users to ask biologically meaningful questions about their data and let them combine and reuse their results to construct and annotate genetic networks. BioNetwork bench is created primarily for biologists interested in acquiring and manipulating information about their genes/proteins/pathways of interest and bioinformaticians conducting research in systems biology, with little or no experience of a database querying language such as SQL.
BioNetwork bench consists of a MySQL database for storing and manipulating gene expression datasets and Cytoscape-format networks paired with an interactive querying engine that allows to iteratively ask questions about expression datasets and annotated genetic networks and to merge and re-use the results obtained.
The Retina Database is a repository for storing protein and gene expression datasets as well as inferred or proposed genetic networks for mouse retina. Since our research is focused on developing retina in mice, the datasets currently present in our database reflect this interest. However, data for any organism or tissue can be stored in the database; the schema used is equally suitable for storing gene/protein expression data and networks for any biological system
The database querying program component, written in Java, was developed as a plugin for Cytoscape. BioNetwork bench works with Cytoscape networks and supports expression data formats used by Cytoscape.