TissueNets HowToBuild

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In order to use the TissueNets program with its python GUI, we need to  
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== TissueNets System ==
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In order to use the programs included in the TissueNets system with its python GUI, we need to have the following programs:
  
 
{| border="1"
 
{| border="1"
 
|- bgcolor="#abcdef"
 
|- bgcolor="#abcdef"
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! Module Name !! What it does !! Contributors !! SVN?<sup>[1]</sup>!!CPack?<sup>[2]</sup>!!CTest?<sup>[3]</sup>!!Download!!Licensing Notes
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! Module Name !! What it does !! Location!! What to Build
 
|-
 
|-
 
| TissueNets
 
| TissueNets
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| Displays biological networks
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| Main TissueNets module, Displays biological networks, Creates Cluto files
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| Creates Cluto files
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| tissuenets/tissuenets
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| [[User:Tsaic|Charlene Tsai]]
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| tissuenets.cpp
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|Y
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|-
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|Y
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| read_cell_types
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|N
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| Extracts all cell types from the input file dynamically
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| [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win32&downloadFile=register_pair.exe&submit=Download win32]  [http://farsight-toolkit.org/mw/scripts/download.php?downloadType=Modules&operatingSystem=win64&downloadFile=register_pair.exe&submit=Download win64]
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| tissuenets/read_cell_types
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|[http://www.apache.org/licenses/LICENSE-2.0 Apache License, Version 2.0]
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| read_cell_types.cpp
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|-
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| readtextfile
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| Reads text file and converts it into the XML that could be used by the main module
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| tissuenets/readtextfile
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| readtextfile.cpp
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|-
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| defineNodes
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| Creates Nodes of the network
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| tissuenets/XQUERY-programs
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| defineNodes.XQUERY (no need to build)
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|-
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| kneighbor
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| Creates links based on k-nearest neighbor algorithm (with exact solution)
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| tissuenets/XQUERY-programs
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| kneighbor.XQUERY (no need to build)
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|-
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| defineNetwork
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| Combines nodes and links and forms a network in [[http://www.cs.rpi.edu/~puninj/XGMML/ XGMML]] form
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| tissuenets/XQUERY-programs
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| defineNetwork.XQUERY (no need to build)
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|-
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| defineHistogram
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| Creates histogram data by using the given feature name and the input file (which is formatted in XML)
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| tissuenets/XQUERY-programs
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| defineHistogram.XQUERY (no need to build)
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|-
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| BioNet
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| 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)
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| tissuenets/
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| bionet.cpp
 
|-
 
|-
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| [[Registration_page#register_joint|register_joint]]
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| tissuenets-py
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| 3D joint Multi-image Registration
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| python GUI for all the programs in the TissueNets system.
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| [[User:Tsaic|Charlene Tsai]]
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| tissuenets/python-GUI-and-other-windows-programs
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|Y
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| tissuenets-py.py (no need to build)
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|Y
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|N
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|}
 
|}
  
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4- Build BioNet (requires libxml2\include)
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== How to Run XQUERY Programs ==
  
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5- In order to run the XQUERY programs:
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* Install Java
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• Install Java
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* Download and install Saxon-B 9.1 from:
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• Download and install Saxon-B 9.1 from:
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http://saxon.sourceforge.net/     (Click on “Download for Java")
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http://saxon.sourceforge.net/
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Click on “Download for Java(2.0 Mbytes)
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Note that I included the required Jar files (saxon9 and others) in bionet directory. They should be sufficient to run XQUERY programs.
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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.
  
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DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE
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(DO NOT install Saxon-SA 9.1 instead. It is NOT OPEN-SOURCE.)
  
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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
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* 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)
  
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7- Install Python 2.6
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* Download and Install Python from http://www.python.org/
  
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TO RUN BioNet
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== To run TissueNets with its Python Interface ==
  
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1- Change directory to bionet
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* Change the directory to where you have all the files
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2- Type :  
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* Type : python tissuenets-py.py
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python bionet.py
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Latest revision as of 17:46, 25 August 2009

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)

To run TissueNets with its Python Interface

  • Change the directory to where you have all the files
  • Type : python tissuenets-py.py
Retrieved from "http://farsight-toolkit.ee.uh.edu/wiki/TissueNets_HowToBuild"
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