TissueNets HowToBuild
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(Difference between revisions)
| Line 7: | Line 7: | ||
| TissueNets | | TissueNets | ||
| Displays biological networks, Creates Cluto files | | Displays biological networks, Creates Cluto files | ||
| − | | tissuenets | + | | tissuenets/tissuenets |
| − | | | + | | tissuenets.cpp |
|- | |- | ||
| − | | | + | | read_cell_types |
| − | | | + | | Extracts all cell types from the input file dynamically |
| − | | tissuenets/ | + | | tissuenets/read_cell_types |
| − | | ( | + | | (read_cell_types.cpp) |
|} | |} | ||
Revision as of 16:07, 25 August 2009
In order to use the TissueNets program with its python GUI, we need to
| Module Name | What it does | Location | What to Build |
|---|---|---|---|
| TissueNets | 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) |
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
