NBrowse
Description
N-Browse is a graphical network browser for the visualization and navigation of heterogeneous molecular interaction data. The latest version of N-Browse (Version 2) runs as either a Java applet in a web browser, or as a Java webstart application (launched/accessed by web browser). N-Browse providing highly dynamic and interactive on-demand access to network data available from a remote server. The N-Browse interface is easy to use and accommodates multiple types of functional linkages with associated information, allowing the exploration of many layers of functional information simultaneously. Although created for applications in biology, N-Browse uses a generic database schema that can be adapted to network representations in any knowledge domain. The N-Browse client-server package is freely available for distribution, providing a convenient way for data producers and providers to distribute and offer interactive visualization of network-based data.
Since May 2009, N-Browse version 2 became available. As of August 2009, N-Browse version became ready for beta testing. N-Browse Beta version 1 has been replaced by version 2.
N-Browse version 2 supports pluggable data adapters. N-Browse 2 does not talk to chado, but a chado data adapter could be written if one wanted to store interactions in chado. N-Browse version 2 currently supports MySQL databases and is integrated with the modMine database web service [link modMine: search, mine and download data from the modENCODE project (www.modencode.org) ]. N-Browse 2 communicates with MySQL databases directly via direct JDBC and can also use vjdbc to connect to databases via http.
N-Browse version 2 can save/export data in a variety of formats. Please visit N-Browse for more information.
Internet Resources
N-Browse
The main N-Browse website, is the where N-Browse can be accessed, along with documentation. The NYU database (accessed from the main web site and is the default database) currently provides access to heterogenous functional data in E. coli, C. elegans, D. melanogaster, and H. sapiens (see the website for details on available datasets).
WormBase and TAIR currently use N-Browse as a graphical interface to molecular interaction data that they provide. Links to the N-Browse GUI at WormBase are available on the Gene Summary pages. TAIR's N-Browse search page can be accessed via the Tools menu on the TAIR home page. The modMine database web service will be providing links to N-Browse in their next release.
N-Browse Version 2 Launch
Launch N-Browse beta version 2 WebStart or try the N-Browse beta version 2 Applet
Or:
Launch directly from the N-Browse Home Page
Documentation
N-Browse Version 1
No longer available and supported from the N-Browse web site - source code can be found on sourceforge N-Browse Version 1 repository
N-Browse Version 2
Downloads
N-Browse Version 1 Source Code Download (tar.gz file)
Download the source from the SourceForge download page.
N-Browse Version 2 Source Code Download
Download the source from the SourceForge download page under the trunk directory.
SVN N-Browse Version 2
N-Browse Version 2 source code is available using Subversion and is available in the GMOD SourceForge repository. You can browse the source code directly here: N-Browse Code
Installation
Installing and configuring the N-Browse client-server package for N-Browse Version 1
1. Download and install the required software (Tomcat, Perl,and MySQL).
2. Download the N-Browse installation package from the SourceForge download page.
3. Configure the install_conf file in the nbrowse_server_client/ directory of N-Browse installation package. Note: This configuration file MUST be modified before installing the N-Browse package. Check README file for more details.
4. Run the install.pl script located in the nbrowse_server_client/ directory:
$ perl install.pl
Installing and configuring N-Browse N-Browse Version 2
No installation/configuration is needed for running the N-Browse Version 2 application itself. Please view system requirements N-Browse Version 2 System Requirements. If you wish to host your own copy of N-Browse, or create your own database, etc., please refer the to the DeveloperDoc.txt file in the source code's doc directory.
Installing and populating the N-Browse generic database
Note the following instructions are common to both N-Browse 1 and 2. The Perl dataloader scripts and README file are located in the nbrowse_dataloader/ directory of the N-Browse installation package.
5. Configure the dataloader_conf file in the nbrowse_dataloader/ directory.
6. Run dataloader perl scripts in the nbrowse_dataloader/ directory. Please see README for the detail information about file formats and HOWTO.
Note for N-Browse 2 users: If you wish to create your own database, the directory server/nbrowse-db contains database scripts, etc. to use. Please refer to sections Data Loaders and Creating your own database in the source code's DeveloperDoc.txt file in the doc directory for more information.
Contacts
Please send questions to the N-Browse_admin. This is the product of Kris Gunsalus' (kcg1@nyu.edu) lab at NYU. Huey-Ling Kao developed N-Browse Version 1. N-Browse Version 2 was initially developed by Victor Chest and by Mark Gibson. It is currently being developed by Monty Schulman.
