The exercises are intended to illustrate the following:
- Problem solving in bioinformatics of immunology using the tools
available on the WWW.
- Selection of tool technology suitable for a given problem.
- Locate on the WWW and download the proteome of
- Identify the secretome part of the proteome.
- Predict the presence of CTL epitopes in the proteins of the secretome.
Identify the 50 potential MHC ligands with the highest prediction scores.
There will be three exercises during which you will perform
the task above three times using three different technologies: traditional
called from a PERL script
) and from
). We will compare
the three technologies and discuss their strengths and weaknesses.
The exercises will be done in groups of two; each group will need
a portable computer with an Ether or wireless network card, a WWW browser,
an SSH client and an X11 server. It will be possible to borrow
such a computer at CBS if your own portable does not meet the requirements.
You will use the temporary accounts created for the workshop on the CBS
computer system. The tools needed for the exercises have been installed
and tested at CBS; however, we will make sure to provide information on
how to obtain all the key tools for later use on your own system.
Functionality to test on Wed, Jan 24, 16:45-17:00
After the last lecture of the day we will test the computers to ensure
a smooth start of the first exercise the following day. Specifically,
we will test the following:
- Network access
There is a large number of Ethernet outlets
in the room; cables will be provided. There is also a wireless LAN in the
building; however, you need to authenticate yourself to use it. A guest user
name and password will be provided.
- Login to the CBS servers
The login will be by SSH, guest user names and passwords will be provided.
The server is 'sbiology.cbs.dtu.dk'; the users logging in via the
wireless LAN should login to 'cell.cbs.dtu.dk' first and from there to
Make sure to login with X11-tunnelling enabled. If you login
from the command line use 'ssh -X server_name'. Finally,
execute the command 'xterm&' to check if the X11 service works OK:
a new terminal window should appear on your screen.
- WWW browser
From 'sbiology' execute the command 'mozilla&'. Check if the browser
responds fast enough to work conveniently.
If time allows try to install SoapUI from
http://www.soapui.org/. It will
be needed in Exercise 2; you can run it from 'sbiology' but it will be
faster on the local host.
There will be support people present to help with the preparations:
The same people will assist you during the exercises.