Spindle prediction

We have developed an adaptor for connecting FuncNet to SpindleP and DORA-Spindle, in order to predict human mitotic spindle proteins.

It’s in the form of a command-line client that sends a query to FuncNet, SpindleP and DORA-Spindle, then integrates and displays the results. You only need to supply a query set; the reference set for the FuncNet part of the procedure is built-in.

In order to download and build it, you need a Subversion client, Java JDK 5+, and Maven 2.1+. Check out the source code like so (all on one line):

svn co https://funcnet.svn.sf.net/svnroot/funcnet/trunk/FuncNet-Spindle

This will create a directory called FuncNet-Spindle. Then change to this directory and type:

mvn clean package

This will download all the required third-party libraries and the FuncNet, DORA and SpindleP WSDLs, generate a load of client code, compile everything, and run some tests. Finally, when all the tests have passed, type:

mvn exec:java

This will run a real joint query across FuncNet, DORA and SpindleP, from a data file in the src/main/resources directory, and display the integrated results in XML format. There’s various options you can set — see the README file for more information.

If you have any suggestions for extending the functionality of this tool, let us know. Or feel free to hack on it yourself and send patches. If you would like to see this functionality available as a web service, let us know, either in the comments field below or by email to mailbox ‘info‘ at domain ‘funcnet.eu‘.