2D Contour Project

Things I need to do:

- remove inverse eS and eH

- remove profile field

- change network when clicked

- rollover event for contours

- add information table

- connect this with contour

Running Contour Application

./Parser Segment_Name 1 2 3 4 5 6 7 8 Project_Name

• Segment_Name - the segment name, relative to the filenames. As in V1IL4CDS.1.eH.txt, you would use V1IL4CDS
• 1 - the number of the file associated with this sequences. As in V1IL4CDS.1.eH.txt, you would use 1
• 2 - Is the buffer enabled with this sequence? More ofter than not it will be 1, if not 0
• 3 - This is always 3
• 4 - Number of layers for eH
• 5 - Number of layers for eS
• 6 - Number of layers for inverse eS
• 7 - Not implemented yet, use the number 10 (Start percentage)
• 8 - Not implemented yet, use the number 10 (End percentage)
• Project_Name - This is just the project name you would like to use

Example:

./Parser segment 1 1 3 20 20 10 10 10 Steelers

** Make sure **

Make sure you save the sequence to both the Database_ESIS and store_sequences, and run the application from Database_ESIS.

If you are unable to run the sequence, make sure it is not already in the database. Delete it using: http://entromics.ccp.pitt.edu/Delete/

MySQL - Genome Sequence

Substring for parts of the sequence:
http://dev.mysql.com/doc/refman/5.1/en/string-functions.html#function_substring-index

Apache/MySQL Install

http://httpd.apache.org/docs/2.0/install.html
cd /usr/local/apache2/bin
sudo -i apachectl start

or
cd /usr/sbin
sudo -i apachectl start

http://www.cyberciti.biz/faq/how-to-install-mysql-under-rhel/

reinstall!!
rpm -qa | grep -i '^httpd-'
sudo -i rpm --allmatches --nodeps -ev mysql-server-5.0.77-4.el5_5.
kill `cat /var/run/mysqld/mysqld.pid`
mysqld_safe --init-file=/home/pmd18/passchange &

Red Hat Admin - SSHD and VNC

How do I change the default port that OpenSSH server uses?

http://magazine.redhat.com/2007/04/16/how-do-i-change-the-default-port-that-openssh-server-uses/

Tunnelling VNC over SSH with PuTTY
http://martybugs.net/smoothwall/puttyvnc.cgi

Entromics Server - Things completed today

Installed gcc, gfortran, LAPACK, BLAS, and GSL

Red Hat Admin - Install Packages

yum search package_name
yum install package_name