TissueNets HowToBuild
| Line 34: | Line 34: | ||
| tissuenets/XQUERY-programs | | tissuenets/XQUERY-programs | ||
| defineNetwork.XQUERY (no need to build) | | defineNetwork.XQUERY (no need to build) | ||
| + | |- | ||
| + | | defineHistogram | ||
| + | | Creates histogram data by using the given feature name and the input file (which is formatted in XML) | ||
| + | | tissuenets/XQUERY-programs | ||
| + | | defineHistogram.XQUERY (no need to build) | ||
|} | |} | ||
Revision as of 16:50, 25 August 2009
In order to use the TissueNets program with its python GUI, we need to have the following programs:
| Module Name | What it does | Location | What to Build |
|---|---|---|---|
| TissueNets | Main TissueNets module, Displays biological networks, Creates Cluto files | tissuenets/tissuenets | tissuenets.cpp |
| read_cell_types | Extracts all cell types from the input file dynamically | tissuenets/read_cell_types | read_cell_types.cpp |
| readtextfile | Reads text file and converts it into the XML that could be used by the main module | tissuenets/readtextfile | readtextfile.cpp |
| defineNodes | Creates Nodes of the network | tissuenets/XQUERY-programs | defineNodes.XQUERY (no need to build) |
| kneighbor | Creates links based on k-nearest neighbor algorithm (with exact solution) | tissuenets/XQUERY-programs | kneighbor.XQUERY (no need to build) |
| defineNetwork | Combines nodes and links and forms a network in [XGMML] form | tissuenets/XQUERY-programs | defineNetwork.XQUERY (no need to build) |
| defineHistogram | Creates histogram data by using the given feature name and the input file (which is formatted in XML) | tissuenets/XQUERY-programs | defineHistogram.XQUERY (no need to build) |
4- Build BioNet (requires libxml2\include)
5- In order to run the XQUERY programs: • Install Java • Download and install Saxon-B 9.1 from: http://saxon.sourceforge.net/ Click on “Download for Java(2.0 Mbytes)
Note that I included the required Jar files (saxon9 and others) in bionet directory. They should be sufficient to run XQUERY programs.
DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE
6- Set the CLASSPATH accordingly so that the required jar files can be found. (If the Jar files are in bionet directory, including bionet in the CLASSPATH will do the job
7- Install Python 2.6
TO RUN BioNet
1- Change directory to bionet 2- Type : python bionet.py
