Forrest Sheng Bao's Cyberhome

by Forrest Sheng Bao http://fsbao.net

Since 2008, I have been helping Dr. Xie, Dept. of Biological Sciences, Texas Tech University on bioinformatics computing. I worked happy with his Post-Doctoral researcher Dr. Qi, who is now with Indiana University. I plan to write down some instructions so that new PhD students can work happy with me as Dr. Qi did.

Workstation software configurations:

• Powered by Ubuntu Linux 7.10. I DO have the plan to upgrade the operating system to latest Ubuntu Linux 9.04, of codename Jaunty Jackalope.
• Able to run Shell (the traditional command line interface), X11 applications (such as Internet surfing in Firefox Web Browser) and transfer files via SFTP.
• FASTA and Python environemtn ready. Other bioinformatics software can be installed upon requests.

How to connect (so that you can use Linux Shell or start GUI programs)?

• On Linux or Mac, open a shell. On Ubuntu Linux, do as follows.
  
• On Windows, google "SSH client" and download whatever you like.
• Connecting to the workstation from your SSH client software. On Ubuntu Linux, type "ssh YOUR_USERNAME@SERVER_ADDRESS" and enter your password as prompted,  like this in the shell (I replaced IP addresses by xxx for security reason. Please ask me for their real values.):

  forrest@dophin:~$ ssh forrest@xxx.xxx.xxx.xxx
  forrest@xxx.xxx.xxx.xxx's password: 
  Linux ESB319 2.6.22-14-generic #1 SMP Tue Feb 12 07:42:25 UTC 2008 i686
  
  The programs included with the Ubuntu system are free software;
  the exact distribution terms for each program are described in the
  individual files in /usr/share/doc/*/copyright.
  
  Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
  applicable law.
  Last login: Sat Apr 18 10:16:42 2009 from xxx.xxx.xxx.xxx

• Go to working directory

  forrest@ESB319:~$ cd /forrest/Xie/
  forrest@ESB319:/forrest/Xie$ ls
  backup_s_9_tag.tar.bz2  s_6_tag  s_7_tag  s_8_tag  s_9_tag  tair8gene
  

 How to start graphic applications?

• Add a "-X" option when you connect to the server, like this: "ssh forrest@xxx.xxx.xxx.xxx -X"
• Type the name of the application and press enter.

How to transfer files?

• On Ubuntu Linux, type "sudo apt-get install filezilla". After installation, go to Applications -> Internet -> Filezilla FTP client. Please ask me for other options.
• On Mac and Windows, go to http://filezilla-project.org/ to download Filezilla client and install. Then start it as you start regular Windows and Mac applications. Please ask me for other options if you not want to or are not able to install a new software.
• Enter the server IP, username and password in filezilla. Set port number to 22. Be sure the set the "remote site" directory as /forrest/Xie
  

If you have any other questions, let me know.