This exercise will help you to set up directories in which you can store information for each homework assignment. You will also learn how to list the files and subdirectories in a directory and how to access these files and subdirectories from your current working directory, and how to make copies of files and put them into the desired directory. All commands necessary to carry out this assignment are found on the website under Helix Commands.

1. Log onto Helix: Steps needed to log onto Helix can be found at http://helix.biostat.utsa.edu/~kgarnett/bioinformatics/connhelix.html .

Change your password using the command passwd. Do not tell your password to anybody.

2. Display a browser:

On a Sun station: Set up the environment for X-windows display, then type netscape& to the helix prompt.

On a PC: Click on the Explorer or Netscape icon.

Go to our website (http://helix.biostat.utsa.edu/~kgarnett/bioinformatics/biopage.html), and follow the links to the Class Notes page (http://helix.biostat.utsa.edu/~kgarnett/bioinformatics/notes4953.html). Go to the pages entitled About Helix and Helix Commands and read them. You may want to print the commands.

3. In Helix, you will be in your Home directory. Make a directory entitled homework. The command necessary to do this is at the website under Helix Commands. Remember that Unix is case sensitive, so it is usually a good idea to use all lowercase letters when naming files and directories at first. Once you have made a homework directory go to it. What command did you use to get to your homework directory? In your homework directory make subdirectories that will be used to hold your information for all ten homework assignments. That is, make a subdirectory for the first homework assignment called "ex1", for the second homework assignment called "ex2", etc.

4. If you are in your homework directory and you want to see a list of files and subdirectories contained in this directory, how would you get this list on the screen; what command(s) would you use?

5. If you are in your homework directory and you want to get into your ex2 subdirectory, how would you do this?

6. How would you get back to your main homework directory from your ex2 subdirectory? How would you get back to your main home directory from your ex2 subdirectory?

7. If you forget what directory you are in, how can you find this out? (What command would you use?).

8. Give the command and pathname for accessing your ex1 subdirectory from your home directory.

9. Working in your ex1 subdirectory make a file called group. Do this in the text editor pico. You will name the file when exiting (control + x) pico. In this file list the names of your group members, their majors, the type of computer that each member will be using, and the e-mail address of each group member (If someone does not have an e- mail address, one will be issued once a Lonestar Account is acquired. Update this file when all e-mail addresses are obtained.). Print a copy of this file.

10. After exiting the text editor, pico, list the elements of ex1 on your screen. What commands did you use? What came up on the screen? If you want to view the file that came up on the screen, how would you do this? (There is more than one way - list two ways).

11. What is the pathname to your home directory? To see this go to your home directory and use the command that allows you to see what directory you are working in. If I have a file called test in my home directory, ~leung, what is the pathname that someone would use to get to this file?

12. From your home directory, make a copy of the file called test in my home directory ,~leung, and put it in your home directory. You will need to use the command necessary to make a copy of a file. You will need to use the pathname necessary to access a file called test in the home directory of ~leung, and the pathname to your home directory. Write down the command and pathname to do this. Write down the content of the file. Put the file into your ex1 subdirectory. Show how you did this.

13. Draw a simple diagram representing the files and directories in your Helix account. See diagram here.