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Structural Biochemistry and Bioinformatics

Introduction to Computer for structural biology/bioinformatics course

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.

Monday

Tutorial

Read this tutorial After this you should be familiar with the following commands:

• &
• <
• >
• grep
• ln
• lpp
• lpq
• lpr
• ls
• less
• more
• cat
• man
• mkdir
• mv
• pwd
• rm
• sort
• |

Emacs

Xemacs is one of the most extensible text editors around. You should read the tutorial (help->Basics->Tutorial).

xmgr

XMGR is an excellent program to create plots, try to make some nice plots.

Misc

Now it is time to spend some time to play, try all the commandos you know, create some files, edit them etc.

Tuesday

Netscape

Many assignments can be done by using netscape, if you have not used netscape before familiarize you with it.

Email

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

Entrez is a very useful site for biological information, if you have not used it before do this assignment.

Entrez

Entrez is a very useful site for biological information, if you have not used it before do this assignment.

Read your NT files from linux

1. Make a directory (for instance mkdir ~/NT)
2. smbmount //server.biokemi.su.se/users ~/NT
3. Type your pasword (for NT)

1. smbumount ~/nt

Make your own home page

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 (on NT) 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:

1. Now your file should be available from the following URL http://private.biokemi.su.se/~username/filename

Make a personal home page, tell who you are and what is fun.

Thursday

Now you should familiarize you with the molecular graphics programs, using NT or Linux

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: The tutorial is available at: http://www.expasy.ch/spdbv/text/tutorial.htm"