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Introduction to the exercises


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.

The problem

  1. Locate on the WWW and download the proteome of Mycobacterium tuberculosis.
  2. Identify the secretome part of the proteome.
  3. 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 paste-and-click services (Exercise 1), SOAP based Web Services called from a PERL script (Exercise 2) and from TAVERNA (Exercise 3). We will compare the three technologies and discuss their strengths and weaknesses.

Practical preparations

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 'sbiology'.
  • X11
    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.
  • SoapUI
    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.



CONTACT

Ole Lund,