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Immunological Bioinformatics - #27685

Information for participants

THIS PROGRAMME IS STILL PRELIMINARY AND MIGHT CHANGE BEFORE THE ACTUAL DATE!


GENERAL DAILY SCHEDULE
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 17 pm.

PLACE: DTU Building 208 room 060 (in the basement)
LITTERATURE: Immunological Bioinformatics, Lund et al., MIT Press 2005. (can be purchased at discount in CBS build. 208) + additional publications



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.

  • For doing some of the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
    See informations on prerequisites on:
    Tools for SSH and X11


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 can be purchased at discount in CBS build. 208


O Monday, June 7

Introduction, immunology brush up, and Unix
9.00 - 9.20
Introduction to the course.
Claus Lundegaard, CBS, DTU Systems Biology.
9:20-10:15
Basic mechanisms of immune defense
Susanne Brix Pedersen, CBS, DTU Systems Biology.
Recording (including breaks...Sorry!)
10.15 - 10.45
Coffee Break
10.45 - 12.00
Basic mechanisms of immune defense continued
12.00 - 13.00
lunch break
13.00 - 13.30
Training and evaluation of predictive methods.
Claus Lundegaard, CBS, DTU Systems Biology.
Recording
Handout
13.30 - 16.00
Exercises: Unix and awk, a crash course
Claus Lundegaard, CBS, DTU Systems Biology.

O Tuesday, June 8
Vaccines, antibodies, and epitopes
9.00 - 9.30
Yesterday's exercise round up
9.30 - 10.15
Vaccines and epitope dicovery.
Claus Lundegaard, CBS, DTU Systems Biology
10.15 - 10.45
Coffee Break
10.45 - 11.15
Antibodies and TCRs, development and selection.
Claus Lundegaard, CBS, DTU Systems Biology.
11.15 - 12.00
DNA Vaccines, plasmids and design
Anders Fomsgaard, MD, DMSc, Chief of Molecular Virology Laboratory, Department of Virology, Statens Serum Institut
Recording.
12.00 - 13.00
lunch break
13.00 - 15.30
Exercises:
 
Databases and web resources in Immunological bioinformatics.
Claus Lundegaard, CBS, DTU Systems Biology.
 
Analysis of immunoglobolin gene rearrangements.
Claus Lundegaard, CBS, DTU Systems Biology.

Wednesday, June 9
T-cell Epitopes
9.00 - 9.30
Yesterday's exercise 1 round up Yesterday's exrcise 2 round up.
9.30 - 10.00
MHC polymorphism, sequences, and population data.
Claus Lundegaard, CBS, DTU Systems Biology
10.00 - 10.30
Coffee Break
10.30 - 12.00
Prediction of MHC peptide binding.
Claus Lundegaard, CBS, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercise:
Prediction of MHC:peptide binding using PSSM and ANN.
Claus Lundegaard, CBS, DTU Systems Biology.

Thursday, June 10
Supertypes, HLA clustering, and integration

9.00 - 9.30
Yesterdays exercise round up.
Recording.
9.30 - 10.15
Supertypes and Clustering
Claus Lundegaard, CBS, DTU Systems Biology.
Recording.
10.15 - 10.45
Coffee Break
10.45 - 11.30
Prediction of proteasome processing and TAP binding; The Class I Pathway.
Handout.
Claus Lundegaard, CBS, DTU Systems Biology.
Recording
11.30 - 12.00
Integration of predictions.
Claus Lundegaard, CBS, DTU Systems Biology.
Recording.
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercises: Development of vaccines against HCV.
Claus Lundegaard, CBS, DTU Systems Biology.

O Friday, June 11
B cell epitope predictions
9.00 - 9.30
Yesterdays exercise round up.
Recording.
9.30 - 10.00
Prediction of B cell epitopes
Claus Lundegaard, CBS, DTU Systems Biology.
Recording
10.00 - 12.00
Exercise: B cell epitope predictions.
Claus Lundegaard + Bent Petersen, CBS, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 13.45
Development of a subunit vaccine against TB
Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute
Recording.
13.45-14.30
Project initiation
Introduction to project work
As Slides
Recording.

O Monday, June 14
Evolution and viral pathogens
  • BACKGROUND TEXTS:  Chapter 3
9.00 - 9.30
Friday's exercise round up.
Recording.
9.30 - 10.15
Mathhematical simulations of HIV infection
Nicolas Rapin, Ph.D., BRIC
Recording.
10.15 - 10.30
Coffee Break
10.30 - 12.00
Molecular Evolution.     Handout exercise
Anders Gorm Pedersen, CBS, DTU Systems Biology.
Recording1.
Recording2.
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercises: Viral Evolution
Anders Gorm Pedersen and Claus Lundegaard, CBS, DTU Systems Biology.
Recording.

O Tuesday, June 15
Symposium with invited speakers
9.30 - 10.00
Yesterdays Exercise roundup
Anders Gorm Petersen, CBS, DTU Systems Biology.
10.00 - 10.30
Coffee Break
10.30 - 11.15
TBA
Magnus Strandh, Symphogen A/S
11.15 - 12.00
MHC Dextramers for detection of antigen specific T-cells
Jørgen Schøller, Ph.D., CSO, Co-founder, Immudex A/S
12.00 - 13.00
Lunch Break
13.00 - 13.45
Epitope grafting and antibody engineering - the molecular basis of the allergic reaction
Kaare Lund, PhD, Manager, Experimental Immunology, ALK-Abello A/S
14.00 - 14.45
Adjuvants in vaccine formulations
Prof. Peter Heegaard, DTU-Vet

O Friday, June 16 to Tuesday, June 22:

Project work


O Wednesday, June 23
Quiz and exercise exam

10.00 - 14.00
Exam 2010.
Quiz and exercize exam.

O Thursday, June 24:     Poster Presentations
Poster Day
9.30 - 10.15
Coffee (10.00) and poster setup
10.15 - 10.45
Prediction of MHC II loading of tissue restricted antigens
10.45 - 11.15
Prediction of Immunogenic Peptides in Ebola- and Marburgvirus
11.15 - 11.45
Constructing a Vaccine Against Human Papillomavirus
12.00 - 13.00
Lunch Break
13.00 - 13.30
Constructing a Vaccine Against Human Papillomavirus
Hepatitis C Virus
13.30 - 14.00
VACCINE FOR THE ZAIRE EBOLAVIRUS
14.00 - 14.30
Mycobacterium tuberculosis
14.30 - 15.00
Course round up


For more information, please contact Claus Lundegaard






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