UNIX Basics in Bioinformatics

Lecture notes for the course

Computer Modeling of Macromolecular Structure and Function
Bioinformatics on the Web

  HBCG 6206/HBCG 6338
January 2008

Prepared by

David Power, Ph.D. Jan. 2008
tdpower@utmb.edu

• A little History of the UNIX operating system
• Definitions used in unix commands
• Everyday UNIX commands
• Listing files and directories
• Making Directories
• Changing to a different Directory
• The directories
• Path names
• Home directory and path name
• Copying Files
• Moving Files
• Removing Files and directories
• Displaying the contents of a file on the screen
• Searching the contents of a file

 
• File systems

• File security and process
• File system security (access rights)
• Changing access rights
• Processes and Jobs
• Listing suspended and background processes
• Killing a process

• Student Computer Room in Clay Hall 205
• bohr.utmb.edu (on the left)
  
• IP Address 129.109.59.104
  
• boyle.utmb.edu (on the right)
  
• IP Address 129.109.59.216
• Clay Hall Computational Facilities
  

• Logins, password, scp and ssh
  
• User password
• Logins
• telnet
• ftp

• Advanced UNIX commands
• Redirection
• Redirecting the output
• Redirecting the input
• Pipes
• Wild cards
• Filename conventions
• Getting help