CytoscapeWeb :: Instructions.

URL: http://cytoscapeweb.cytoscape.org/


Downloaded version 0.7.2

$ unzip cytoscapeweb_v0.7.2.zip

svn checkout http://chianti.ucsd.edu/svn/cytoscapeweb/trunk cytoscapeweb-all-read-only

Cytoscape :: Plugins :: Download

Plugins > Manage Plugins > Keyword search for plugin

Downloading plugin for Multicolored Node, where each node is divided into pie depending on the attribute. Additional notes is present at http://groups.google.com/group/cytoscape-discuss/browse_thread/thread/12ccc21ae5756778

To download and install a plugin
Go to

$ cd ~/Cytoscape_v2.8.1/plugins
$ wget http://url.to.site/multicolor

Restart Cytoscape to include it in Cytoscape.

A rainbow wheel named color nodes should appear on top of the window.

Intersting Plugins:
Venn Diagram: http://www.dishevelled.org/venn-cytoscape-plugin/
User-defined: http://www.genmapp.org/BubbleRouter/manual.htm

Qiime : Install : HPC

on TALON,
check if python is available

$ what python
/usr/bin/python

Installing Dependencies required for all features of Qiime.
1. Numpy 1.3.0
Source: http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.tar.gz/download
Dependencies:
1.A. Nose

$ wget http://somethingaboutorange.com/mrl/projects/nose/nose-1.0.0.tar.gz
$ tar zxvf nose-1.0.0.tar.gz 
$ python setup.py install --prefix=$HOME/bin/python

Edit ~/.bashrc and enter the line below

export PYTHONPATH=$PYTHONPATH:$HOME/bin/python

Refresh bash, and check the installation of Nose

$ source ~/.bashrc
$ python -c "import nose"

Untar and install Numpy

$ tar zxvf numpy-1.3.0.tar.gz
$ cd numpy-1.3.0

Download PyCogent-1.5 from http://sourceforge.net/projects/pycogent/files/PyCogent/1.5/PyCogent-1.5.tgz/download
Unpacking and Installing

$ tar zxvf PyCogent-1.5.tgz
$ cd PyCogent-1.5

what

Ruby :: rsruby

On MAC OS

$ sudo gem install rsruby -- --with-R-home=/usr/lib/R --with-R-include=/usr/share/R/include --with-R-dir=/Library/Frameworks/R.framework/Resources/

After installation setup the R_HOME global variable

export R_HOME=/usr/bin/R

At IRB

>> require 'rsruby'
=> true
>> RSRuby.instance
cannot find system Renviron
Fatal error: unable to open the base package

Ruby :: Kappa :: Installation

Information regarding Kappa
http://psilambda.com/

Installation on Ubuntu 10.10
- Download Jockey from https://launchpad.net/jockey
- To build it you need python-distutils-extra at https://launchpad.net/python-distutils-extra
$ cd  python-distutils-extra-2.22
$ ./setup.py build
$ sudo ./setup.py install


In Jockey the ../setup.py is giving errors
$ sudo apt-get install python-encutils

Tryptophan biosynthesis pathway

Enzymes present in Tryptophan biosynthesis pathway.

1. Anthranilate synthase
2. Anthranilate PR-transferase
3. PR-anthranilate isomerase
4. Indole-3-glyserol phosphate synthase
5. Trp synthase
6. Tryptophan aminotransferase

Tryptophan synthase beta chain
Tryptophan synthase alpha chain
Tryptophanase
COG0134 Indole-3-glycerol phosphate synthase
COG0133 Tryptophan synthase beta chain
COG0159 Tryptophan synthase alpha chain
COG3033 Tryptophanase

Library check

TO check for libraries needed for the package

$ ldd rmblastn 
    linux-vdso.so.1 =>  (0x00007fff5b9e4000)
    libz.so.1 => /lib/libz.so.1 (0x00007f7e7c416000)
    libdl.so.2 => /lib/libdl.so.2 (0x00007f7e7c212000)
    libpcre.so.0 => not found
    libnsl.so.1 => /lib/libnsl.so.1 (0x00007f7e7bff7000)
    libpthread.so.0 => /lib/libpthread.so.0 (0x00007f7e7bdda000)
    libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f7e7bac5000)
    libm.so.6 => /lib/libm.so.6 (0x00007f7e7b842000)
    libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f7e7b62b000)
    libc.so.6 => /lib/libc.so.6 (0x00007f7e7b2a7000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f7e7c63c000)

This tells you that libpcre.so.0 library is missing.