N-Browse
Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools
Abstract N-Browse is an interactive graphical browser for molecular interaction networks/biological networks.
The goal of N-Browse is to provide a simple, intuitive, and dynamic interface to molecular interaction data that allows biologists to take advantage of the rapidly expanding body of functional genomics data.
The N-Browse server at New York University (NYU) currently provides access to a variety of large-scale functional genomic datasets from several species.
Users can also upload their own data for integrated browsing with publicly available datasets.
The N-Browse graphical user interface (GUI) runs as a desktop webstart application that launches from your web browser and uses a client-server system to provide network data to the user from a server-side database.
It uses Java Database Connectivity (JDBC) to talk to a MySQL database with the optimized N-Browse schema.
There is a Data-Adapter interface (which the JDBC adapter implements) that allows developers to hook up their data-source to N-Browse.
N-Browse uses a flexible data model that is optimized for retrieval and display of network data.
While it was designed specifically with biological data in mind, the concept behind N-Browse is to create a “Generic Network Browser” capable of handling any type of network-based data and associated information.
The N-Browse client-server package is designed for portability, with the goal that multiple independent N-Browse systems could be set up to provide graphical interfaces for network-based data from different data sources.
The N-Browse GUI contains five (5) main parts:
1) Main Menu & Navigation --
Main Menu & Navigation provides options to manipulate the Graph Display Panel (see below...).
- a) The File Menu provides file and graph editing options, as well as view and help access.
- It provides access to saving & loading N-Browse binary sessions and N-Browse text-based files. The File menu also provides image exporting and graph printing.
- b) The Edit Menu currently provides access to the Edge Weights View (The Edge Weights View provides the user the ability to use a weighted edge layout for generating graphs).
- In the future, it can be used for preferences and image copying, etc.
- c) The View Menu is used to provide access to any closed or unopened views/tabs available in N-Browse.
- d) The Help Menu provides access to the tutorial web information and the About Dialog (including version number).
2) Graph Display Panel --
The Graph Display Panel provides a network representation of available interaction data. It offers a number of interactive features for manipulating the graph and communicates with Node & Edge Data.
Additional aspects of the display layout can be controlled using the Main Menu & Navigation.
3) Node & Edge Data --
Node & Edge Data contains two (2) main sections, which can be opened by selecting the corresponding tab:
- a) Node Info - provides a brief description and some useful links about a particular gene in the graph.
- b) Edge Info - provides gene interaction information, along with dataset information.
- c) GO Term - Displays the Gene Ontology (GO) directed acyclic graph (DAG) and highlights terms for gene(s) in the current graph.
4) Graph Display Options --
Graph Display Options contains two (2) main sections, which can be opened by selecting the corresponding tab:
- a) Edge Filter - provides a brief description and some useful links about a particular gene in the graph.
- b) Node Attribute - allows you to select node attributes to be highlighted on the graph.
5) Upload User Defined Data --
- a) There are four (4) different formats provided for user-defined data and Cytoscape, Simple Interaction File (SIF) files can also be uploaded.
Note 1: As of August 2009 - A new version of N-Browse is ready for beta testing. NBrowse2 is a major reimplementation of N-Browse.
Note 2: As of September 2010 - N-Browse is now integrated with the modMine database web service.
System Requirements
Contact manufacturer.
Manufacturer
- Department of Biology
- Center for Comparative Functional Genomics
- New York University
- 100 Washington Square East
- New York, NY 10003-6688 USA
- Tel: (212) 998-8200
- Fax: (212) 995-4015
- E-Mail: biology@nyu.edu
Manufacturer Web Site N-Browse
Price Contact manufacturer.
G6G Abstract Number 20707
G6G Manufacturer Number 104279