TissueNets HowToBuild

TissueNets System

In order to use the programs included in the TissueNets system 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)
BioNet	This is the older version of the main TissueNets module. We use it to create minimum spanning trees (will be removed in the near future)	tissuenets/	bionet.cpp
tissuenets-py	python GUI for all the programs in the TissueNets system.	tissuenets/python-GUI-and-other-windows-programs	tissuenets-py.py (no need to build)

How to Run XQUERY Programs

• Install Java
• Download and install Saxon-B 9.1 from:

http://saxon.sourceforge.net/ (Click on “Download for Java")

Note that we have included the required Jar files (saxon9 and others) in \trunk\tissuenets\python-GUI-and-other-windows-programs directory. They should be sufficient to run XQUERY programs.

(DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE.)

• Set the CLASSPATH accordingly so that the required jar files can be found. (If the Jar files are in the current directory, including it in the CLASSPATH will do the job)

• Download and Install Python from http://www.python.org/

To run TissueNets with its Python Interface

• Change the directory to where you have all the files
• Type : python tissuenets-py.py