biographd
BioGraph computing kernel daemon
Provides an XMLRPC service to compute pageranks, find related entities, find paths between entities, from entities or entity sets, does comparisons between collections. An example client library for ruby (biographclient.rb) and test client (client.rb) are provided.
About Biograph
Biograph (developed at UA and VIB) is a web service that integrates biomedical knowledge bases and allows researchers to relate various biomedical concepts to candidate targets, for example to investigate potential genetic candidates for hereditary diseases, or to find chemical compounds to target disease-related proteins. Biomedical relations among seemingly unrelated concepts are supported by relevant automated functional hypotheses.
Please refer to our open access journal paper for more information about Biograph:
A.M.L. Liekens, J. De Knijf J, W. Daelemans, B. Goethals, P. De Rijk, J. Del-Favero J, BioGraph: Unsupervised Biomedical Knowledge Discovery via Automated Hypothesis Generation, Genome Biology 12:R57, 2011.
The source code for Biograph is hereby made available under a GPL v3 license.
Requirements
- XMLRPC for C: http://xmlrpc-c.sourceforge.net/
- Mysql Connector Client C++: http://dev.mysql.com/tech-resources/articles/building-mysql-connector-cpp.html
- TODO: requires tweaking of Makefile for correct path of mysqldev & mysqlconnector
Compile it
- Copy
mysqlconfig.h.sampletomysqlconfig.hand configure - Run
make
Run it
- Start
./biographd - Test with
./client.rb- TODO: know where the mysql database is, now hardcoded