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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.
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You can access to web version of BEReX (iBEReX)
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1. Program availability and requirements
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- Operating systems : Windows, Mac, Linux
- Java runtime : JRE6 or higher is need to run the application
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2. Installation
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- 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:
- Windows : berex-v1-windows.zip(184MB)
- Mac : berex-v1-mac.zip(184MB)
- 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
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3. Documentation
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User Guide : BEReX v1.0 User Guide
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4. Souce Code
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Source Code : berex_sourcecode.zip
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5. License
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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
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6. Contact - for bugs, comments and questions
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Minji Jeon: mjjeon@korea.ac.kr
Jaewoo Kang: kangj@korea.ac.kr
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Last updated on May 21, 2014
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