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

Red Hat Admin - New User

useradd new_username
passwd new_username
chage -d 0 new_username

Cygwins/C/MySQL

Summer work to be completed

1. Order/Setup server for Entromics project
2. Connect Server to PittGrid
3. Update scripts to use Server
4. Write up ESIS for May 25th (Dr. Pancoska back in Pittsburgh)
5. June 3rd/4th conference in San Antonio
6. July 9th Poster presentation
7. Help write up job description