In this course we will two different operating systems, linux and Windows-NT.To switch between the operating systems you need to restart the computer (This is easiest done by pressing "Ctrl-Alt-Del" at the same time). Then at the boot prompt you type linux for linux and NT for windows-NT. Many tasks can be performed independently of the operating system however there are some tasks where one of the operating systems work better. During most of the bioinformatics exercises it is necessary to use linux, while it is better to use NT to view structures.
The first week you will familiarize you with the computers. It should not be too difficult as most program can be started from menus (from the start-bottom in the left down corner). In linux you will need to know some shell-commands to run all programs.
Read this tutorial After this you should be familiar with the following commands:
Emacs is one of the most extensible text editors around. You should read the tutorial (help->Basics->Tutorial).
XMGR is an excellent program to create plots, try to make some nice plots.
gimp and xv are two nice programs for graphic creation.
Now it is time to spend some time to play, try all the commandos you know, create some files, edit them etc.
Many assignments can be done by using netscape, if you have not used netscape before familiarize you with it.
We recommend that you use netscape to read your email. It shall be configured the same from NT and linux. You need to configure your email address, pop server etc. Ask the supervisors how to do that. Try to send an email to yourself, to a friend etc. Try sending an email with a picture attached to yourself.
Entrez is a very useful site for biological information, if you have not used it before do this assignment.
Now it is time to create your own home page. It is easiest done by using netscape. Just select edit page. If you create a catalog in your home directory called public_html/ and save your homepage there it is accessible from the www-server. If you tell that it should be seen from the outside. Easiest done by:
Make a personal home page, tell who you are and what is fun.
Now you should familiarize you with the molecular graphics programs, using NT
The program we will use is called "Swiss PDB Viewer". You can run it by clicking on the appropriate icon. It looks quite daunting at first, but it's actually a quite simple and powerful tool for analyzing structures on a personal computer. In order to familiarize yourself with the basic commands and mouse operations for manipulating and displaying molecules, you should follow the tutorial at: http://macweb.acs.usm.maine.edu/chemistry/GR/GraphicsGallery/SPdbV26tut.html Then, if you have time for learning more advanced features, try the tutorial at: http://www.expasy.ch/spdbv/text/tutorial.htm"