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BEReX : Biomedical Entity-Relation eXplorer

 BEReX is a new biomedical knowledge integration, search, and exploration tool. BEReX integrates eight popular databases (STRING, DrugBank, KEGG, PharmGKB, BioGRID, GO, HPRD, and MSigDB) and delineates an integrated network by combining the information available from these databases. Users search the integrated network by entering keywords and BEReX returns a sub-network matching the keywords. The resulting graph can be explored interactively. BEReX allows users to find the shortest paths between two remote nodes; find the most relevant drugs, diseases, pathways and so on, related to the current network; expand the network by particular types of entities and relations; and modify the network by removing or adding selected nodes. BEReX is implemented as a stand-alone Java application.
 

1. Program availability and requirements

 
 

  • Operating systems : Windows, Mac, Linux
  • Java runtime : JRE6 or higher is need to run the application

 
 

2. Installation

 
 

  • Install JRE(skip this step if you have JRE 6 or later, or JDK 1.6 or later)
  • Download BEReX (v.1.0) and unzip the package file:
    1. Windows : berex-v1-windows.zip(184MB)
    2. Mac : berex-v1-mac.zip(184MB)
    3. Linux : berex-v1-linux.zip(184MB)
  • Run BEReX.bat (for Windows) or BEReX.sh.command (for Mac) or BEReX.sh (for Linux)
  • Please cite the following article when using BEReX.
    • Jeon,M., Lee,S., Lee,K., Tan,A., Kang,J.; BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics (2013) doi: 10.1093/bioinformatics/btt598

 
 

3. Documentation

 
User Guide : BEReX v1.0 User Guide
 

4. Souce Code

 
Source Code : berex_sourcecode.zip
 

5. License

 
BEReX is licensed under the GNU General Public License and is 100% freely available to both commercial and academic users. See the file LICENSE.txt in the BEReX distribution package or this URL for the full text of the license: http://www.gnu.org/licenses/gpl.html
 

6. Contact – for bugs, comments and questions

 
Minji Jeon: mjjeon@korea.ac.kr
Jaewoo Kang: kangj@korea.ac.kr

Last updated on Sep 25, 2013
December 6th, 2013 | Tags: , | Category: 生物信息

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