BioStatistics :: DataSet :: Compare

Kolmogorov-Smirnov Test

Summary:
The Kolmogorov-Smirnov test (KS-test) tries to determine if two datasets differ significantly. The KS-test has the advantage of making no assumption about the distribution of data. (Technically speaking it is non-parametric and distribution free.) Note however, that this generality comes at some cost: other tests (for example Student's t-test) may be more sensitive if the data meet the requirements of the test. In addition to calculating the D statistic, this page will report if the data seem normal or lognormal. (If it is silent, assume normal data at your own risk!) It will enable you to view the data graphically which can help you understand how the data is distributed.

In English:
Comparing two data sets, it draws plots to show the difference.

Link:

Click here to enter data for the KS-test

Ubuntu :: Create :: Subversion

On Ubuntu

$ sudo apt-get install subversion

Working directory

~/Desktop/TEST

Create a repository

$ svnadmin create svnroot

- creates a directory called svnroot

$ ll svnroot

drwxr-xr-x 2 localuser localuser 4096 2010-05-06 16:22 conf

drwxr-sr-x 6 localuser localuser 4096 2010-05-06 16:22 db

-r--r--r-- 1 localuser localuser    2 2010-05-06 16:22 format

drwxr-xr-x 2 localuser localuser 4096 2010-05-06 16:22 hooks

drwxr-xr-x 2 localuser localuser 4096 2010-05-06 16:22 locks

Files of interest

$ cat conf/passwd

[users]

harry = harryspassword

dolly = dollyspassword

$ cat conf/svnserve.conf

[general]

## restrict access to read, write and none

harry = write

## password-db is the location of the /path/to/passwd file

password-db = passwd

Now create another svn root, this is not req, but same as above

$ svnadmin create projectx

$ mkdir gsv gsv/trunk gsv/branches gsv/tags

$ cd gsv

$ svn import . file:///home/krevanna/Desktop/TEST/SVN/projectx -m 'initial repository structure'

$ cd ..

There are several ways to checkout svn
- using file://
- this will create the folder called trunk if no name is specified in the end.

$ svn checkout file:///home/krevanna/Desktop/TEST/SVN/projectx/trunk .

- using svn ://

This is to access within the same server

It depends upon the projects involved. If the projects are related, and are likely to share data, then it's best to create one repository with several subdirectories like this:

$ svnadmin create /repo/svn
$ svn mkdir file:///repo/svn/projA
$ svn mkdir file:///repo/svn/projB
$ svn mkdir file:///repo/svn/projC

If the projects are completely unrelated, and not likely to share data between them, then it's probably best to create separate and unrelated repositories.

$ mkdir /repo/svn
$ svnadmin create /repo/svn/projA
$ svnadmin create /repo/svn/projB
$ svnadmin create /repo/svn/projC

Reference:

 http://wiki.site5.com/SVN/Subversion_%28SVN%29_Setup_Guide
 https://help.ubuntu.com/community/Subversion

Ubuntu :: Hostname :: Change

Steps to change the computer hostname to BIOINFO-001

Check for current hostname

$ hostname

Simple steps to change hostname

$ hostname BIOINFO-001

If above steps dont work, then

Edit /etc/hostname

Enter BIOINFO-001

Edit /etc/hosts

Enter BIOINFO-001 after 127.0.0.1

Java :: Binary :: local

Solution
- website: http://www.java.com/en/download/manual.jsp
- downloaded  Linux (self-extracting file)  or Linux 64 for 64 bit machine
- put it in /scratch/kvr0011/packages/

$ sh jre-6u19-linux-i586.bin
$ cd  jre1.6.0_19/bin/
java executable is present here

Providing the path to java binary in the talon job, ran the java package.

Shell :: Command-line arguments

$0 is the name of the command
$1 first parameter
$2 second parameter
$3 third parameter etc. etc
$# total number of parameters
$@ all the parameters will be listed

Bio :: Large Data :: Transfer

http://blogs.nature.com/news/thegreatbeyond/2010/04/improving_the_portability_of_d_1.html

Install :: Ruby

Download Ruby source code

$ wget ftp://ftp.ruby-lang.org//pub/ruby/ruby-1.9-stable.tar.gz

$ tar zxvf ruby-1.9-stable.tar.gz

To configure Ruby, if you are not superuser

$ ./configure --prefix=$HOME/bin

By default it installs in /usr/local/bin

$ ln  -s bin/irb irb

To access irb from any location.