CBS >> CBS Courses >> Immunological Bioinformatics >> Course Programme 2006

INTERNET TRANSMITTED version of Immunological Bioinformatics - #27685

Information for participants

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GENERAL DAILY SCHEDULE
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 16 pm.

For the afternoon exercises you are supposed to log on to CBS' central servers using the User ID and password forwarded to you in an email.
log on to 'organism.cbs.dtu.dk'
- via ssh as described below.

LITTERATURE: Immunological Bioinformatics, Lund et al., MIT Press 2005.

PROGRAMS AND TOOLS

Flash 6 or better
For following the lectures you need a browser with Flash 6 or better. Flash is freeware and can be downloaded by clicking on the link above
UNIX - Beginner's Guide to UNIX is available on-line.
SSH - Secure Shell - from www.ssh.com
For doing the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
If you use windows you can download a non-commercial version of ssh by clicking on the link above and do the following:
- Make a standard install and start the SSH client.
- Add a new profile - name it CBS.
- Edit the profile. On the 'Connection' tab use 'genome.cbs.dtu.dk' as host name and your assigned user ID as user name (example: phd33). Compression should be set to 'zlib' and terminal answerback to 'Xterm', press OK.
- Edit the profile again choose this time the 'Tunneling' tab. Mark the checkbox 'Tunnel X11 connections' and press OK. In case you want to get smart and do both 'Connection' and 'Tunneling' tabs at the same time - don't - it does not work.
- Save your settings (the floppy).
- Whenever you want to connect to the CBS server you just start the SSH client and choose the CBS profile and write your password. First time you connect you are asked to accept a server key - just do it.
If you use unix or Mac OS 10 SSH is (or should be) built into your system and we assume you know your own system, so it will not be covered here.
X-Server
You also need a X-server running to see the unix GUI (grafical interface). Any X-server running on your computer will do. If you don't have one, then we provide one here, which you can use for the duration of the course. Please remember to uninstall the x-server when the course is over.
The X-server must be running if you want to use X (clustalW, nedit, etc.) on the CBS server.
We recommend X-win32 and have provided links for installation below.
Download special X-win32.
- You need a license when installing this software. Write your password here:
- Do a standard install using the license.
- When you run the program then a dialog will pop up. Either cancel the dialog box or fill it out with anything plausible. Filling it out once will stop the dialog from appearing again. The data is not used for anything in this setup, the software just thinks it needs it.
- When you are running a small blue X will appear in your systray.

Course Programme
Please note that the programme is updated on a daily basis - click the 'refresh' button once in a while to make sure that you have the most updated information

LITTERATURE: Immunological Bioinformatics, Lund et al., MIT Press 2005.

- Click on the day to open the Breeze Live sessions
- Links to any additional Background Texts might be included under the individual days (the links are currently being updated and more will be added as the course proceeds).
- Links to recordings of the day's lectures will be added at the end of the day.

Tuesday, June 6

Introduction and immunology brush up
Recordings: Introduktion Sylvester-Hvid 1 Sylvester-Hvid 2
Exercise

BACKGROUND TEXTS: Chapters 1+12

9.00 - 9.45: Introduction to the course
Ole Lund, Claus Lundegaard, Morten Nielsen, CBS
9.45 - 10.00: coffee break
10.00 - 10.45: The immune system.
Christina Sylvester-Hvid, Wiborg Biotech Consulting, ApS.
10.50 - 12.00: Cellular Immunity.
Christina Sylvester-Hvid, Wiborg Biotech Consulting, ApS..
12.00 - 13.00: lunch break
13.00 - 15.00: Exercises:

Databases and web resources in Immunological bioinformatics. Ole Lund + Morten Nielsen, CBS

Wednesday, June 7

Pathogens, vaccines and antibodies
Recordings: Lund Lund Lundegaard Lund Exercise

BACKGROUND TEXTS: Chapters 2+10+13 Background immunology from Janeway(Start from the top of the linked page)

9.00 - 9.30: Challenges to the Immune System PowerPoint Slides
Ole Lund, CBS
9.35 - 10.00: Conventional Vaccines
Ole Lund, CBS
10.00 - 10.15: Coffee Break
10.15 - 10.45: Antibodies I, Slides: PowerPoint
Claus Lundegaard, CBS
10.50 - 11.20: Antibodies II, Slides
Claus Lundegaard, CBS
11.25 - 12.00: HLA Diversity and Evolution PowerPoint Slides
Ole Lund, CBS
12.00 - 13.00: lunch break
13.00 - 15.00: Exercises:

Analysis of immunoglobolin gene rearrangements. Claus Lundegaard and Morten Nielsen, CBS

Thursday, June 8

Epitope discovery
Recordings: Blicher Lambert Harndal Vennestrøm Nielsen Exercise

BACKGROUND TEXTS: Synthetic and natural non-live vectors: rationale for their clinical development in cancer vaccine protocols

9.00 - 9.30: T-Cell epitope discovery.
Thomas Blicher, CBS
9.35 - 10.00: Generation of recombinant MHC and peptide competition (RIA) assays.
Kasper Lamberth, IMMI, Universitu of Copenhagen
10.00 - 10.15: Coffee Break
10.15 - 10.45: Recombinant MHC - peptide binding assays using Elisa and Alpha Screen.
Mikkel Harndal, IMMI, University of Copenhagen
10.50 - 11.20: Epitopes in diagnostics.
Jean Vennestrøm, CBS
11.25 - 12.00: Structures and Homology modelling PowerPoint slides
Morten Nielsen, CBS
12.00 - 13.00: Lunch Break
13.00 - 15.00: Exercises: Unix crash course. Ole Lund + Morten Nielsen, CBS

Friday, June 9

Phylogeny and epitope escape
Recordings: Lundegaard Pedersen Exercise

BACKGROUND TEXTS: Chapters 3+4

9.00 - 10.00: Biological Sequence Analysis Keynote Slides PowerPoint Slides
Claus Lundegaard, CBS
10.00 - 10.15: Coffee Break
10.15 - 12.00: Maximum likelyhood phylogeny slides
Anders Gorm Pedersen, CBS Handout exercise
12.00 - 13.00: Lunch Break
13.00 - 17.00: Exercises:
Viral Evolution, Anders Gorm Pedersen + Claus Lundegaard, CBS

Monday, June 12

DNA Arrays, Neural Networks and Class I processing
KESMIR IS PARTLY WITHOUT SOUND.
Recordings: Jarmer Lundegaard Kesmir Kesmir_repeat_part_1 Kesmir_repeat_part_2 Exercise

BACKGROUND TEXTS: Chapters 5+7+9

9.00 - 10.00: DNA Arrays
Hanne Jarmer, CBS
10.00 - 10.15: Coffee Break
10.15 - 10.45: Neural Networks.
Claus Lundegaard, CBS.
10.50 - 12.00: Prediction of proteasome processing and TAP binding; The Class I Pathway PowerPoint Slides
Can Kesmir, Theoretical Biology Group, Utrecht University in the Netherlands.
12.10 - 13.00: Lunch Break
13.00 - 16.00: Exercises:
Proteasome and TAP predictions, Morten Nielsen + Can Kesmir, Theoretical Biology Group, Utrecht University in the Netherlands.

Tuesday, June 13

Hidden Markov Models and T-cell Epitope prediction
Recordings: Nielsen Nielsen Larsen Exercises

BACKGROUND TEXTS: Chapters 6 + 8

9.00 - 10.00: HMMs PowerPoint Slides
Morten Nielsen, CBS
10.00 - 10.15: Coffee Break
10.15 - 11.00: Prediction of MHC binding peptides using neural networks PowerPoint Slides
Morten Nielsen, CBS
11.15 - 12.00: Selection of Epitopes using an integrative approach Slides
Mette Voldby Larsen, CBS
Small exercise
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises:
Prediction of T cell epitopes, Claus Lundegaard and Morten Nielsen, CBS

Wednesday, June 14

Vaccine design and conformational epitopes
Recordings: Tang Lund Andersen Exercises

BACKGROUND TEXTS: Chapters 11+14

9.00 - 10.00: Selection of potential TB T-cell epitopes. Slides
Sheila Tang, CBS
10.00 - 10.15: Coffee Break
10.15-11.00: Vaccine design. PowerPoint Slides
Ole Lund, CBS
11.05 - 12.00: Prediction of linear and conformational epitopes,power-point slides
Pernille Haste Andersen, CBS
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises:
Prediction of B cell epitopes, Jens Erik Pontoppidan Larsen + Pernille Haste Andersen, CBS

Thursday, June 15

Vaccine Design
Recordings:

BACKGROUND TEXTS:

9.00 - 12.00: Exersices:
Plasmid design, Vaccine design, Gene Atlases, Claus Lundegaard + Morten Nielsen, CBS
12.00 - 13.00: Lunch Break
13.00 -
Introduction to project work , Claus Lundegaard, Morten Nielsen and Ole Lund, CBS
Formation of groups and selection of subjects. Word Document RTF document.

Friday, June 16 - Thursday, June 22: Project work and inwited speakers

Friday, June 16

Recordings: Nansen

9.00: DNA Vaccines.
Anneline Nansen, Statens Serum Institut (SSI).

Monday, June 19

Recordings: Seppälä

13.00: Vaccination against allergy.
Ulla Seppälä, ALK-Abelló

Tuesday, June 20

9.00: The use of bioinformatics in the generation of recombinant polyclonal antibodies.
Peter Sejer Andersen, Ph.D., Symphogen A/S: MOVED TO THURSDAY!

Wednesday, June 21

Recordings: Dohorty

9.00: TB Vaccines.
Dr. T. Mark Doherty, Statens Serum Institut.

Thursday, June 22

Recordings: Andersen Hviid

9.00: The use of bioinformatics in the generation of recombinant polyclonal antibodies.
Peter Sejer Andersen, Ph.D., Symphogen A/S
14.00: Reproductive Immunology or Why did your mother not reject you?
Thomas V. F. Hviid, Ph.D, Staff Specialist, Roskilde University Hospital

Friday, June 23

Poster presentations, examination, round up.
Recordings:

9.00-9.30 Presentation by internet group in 210/168
9.45-10.15 Poster Presentation, Group B
10.15-10.45 Poster Presentation, Group A
10.45-11.15 Poster Presentation, Group C
11.15-11.45 Poster Presentation, Group D: Lunch Break
13.00-13.30 Poster Presentation, Group E
13.30-14.00 Poster Presentation, Group F

For more information, please contact Claus Lundegaard.

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This file was last modified Friday 23rd 2006f June 2006 05:52:53 GMT

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