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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: All litterature will be available through CampusNet



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: All litterature will be available through CampusNet


O Monday, June 6

Introduction, immunology brush up, and Unix
9.00 - 9.30
Introduction to the course.
Claus Lundegaard, CBS, DTU Systems Biology.
Project description
Introduction to project work
As Slides
Recording.
9:30-10:15
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 7
T-cell Epitopes
9.00 - 9.30
Yesterday's exercise round up
9.30 - 12.00
Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN)
MHC polymorphism, sequences, and population data.
Allele-specific versus pan-specific prediction methods
Does processing matter?
Rational epitope discovery using immunoinformatics
A little on MHC class II binding
Morten Nielsen, CBS, DTU Systems Biology
Coffee Break at some point around 10.30
Prediction of MHC peptide binding Powerpoint slides. PDF.
Morten Nielsen, CBS, DTU Systems Biology.
Recording 2 --- Recording 1
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercise:
Prediction of MHC:peptide binding using PSSM and ANN.
Morten Nielsen, CBS, DTU Systems Biology.

O Wednesday, June 8
Vaccines, antibodies, and epitopes
9.00 - 9.30
Yesterdays exercise round up.
Recording
9.30 - 10.15
Vaccines and epitope dicovery.
Claus Lundegaard, CBS, DTU Systems Biology
Recording
Adjuvants
Prof. Peter Heggaard, DTU-Vet
Recording
10.45 - 11.15
Antibodies and TCRs, development and selection.
Claus Lundegaard, CBS, DTU Systems Biology.
Recording 1
Recording 2
11.15 - 12.00
lunch break
12.00 - 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.

O Thursday, June 9
Supertypes, HLA clustering, and integration

9.00 - 9.30
Yesterday's exercise round up recording
Yesterday's exrcise 2 round up.
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.
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 10
B cell epitope predictions
9.00 - 9.30
Yesterdays exercise round up.
NetMHCpan sheet
NetMHCIIpan sheet
Recording.
Claus Lundegaard, Center for Biological Sequence Analysis, DTU Systems Biology.
9.30 - 10.00
Prediction of B cell epitopes
Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.
Recording
10.00 - 12.00
Exercise: B cell epitope predictions.
Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.
Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 13.45 NOTE: Prof. Doherty could not make it this year, so we will watch the recording from last year.
Development of a subunit vaccine against TB
Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute
Recording.
13.45-
Project work
Claus Lundegaard, Center for Biological Sequence Analysis, DTU Systems Biology.

O Tuesday, June 14
Evolution and viral pathogens
  • BACKGROUND TEXTS:  Chapter 3
9.00 - 9.30
Friday's exercise round up.
Recording.
9.30 - 10.15
Prediction of immunogenicuty of therapeutic proteins
Jens Vindahl Kringelum, M.Sc., CBS
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 Wednesday, June 15 to Tuesday, June 21:
Project work
O Wednesday, June 22
Quiz and exercise exam

10.00 - 14.00
Exam 2011.
Quiz and exercize exam.
--
--
14.00 - 17.00
Poster Setup

O Thursday, June 23:     Poster Presentations
Poster Day
9.30 - 10.00
Coffee (10.00) and poster viewing
10.00 - 10.15
Poster Group 6
10.20 - 10.35
Poster Group 8
10.40 - 10.55
Poster Group 3
11.00 - 11.15
Poster Group 1
11.20 - 11.35
Poster Group 2
11.40 - 11.55
Poster Group 4
12.00 - 13.00
Lunch Break
13.00 - 13.15
Poster Group 5
13.20 - 13.35
Poster Group 7
13.40 - 14.00
Poster Group 9

O Friday, June 24
Special guest speaker
10.00 - 11.00
Jared Patch
TBA
11.00-11.30
Claus Lundegaard
EIR Sciences, A DTU Systems Bilogy spin off.
11.30 - 12.00
Course round-up and goodbye


For more information, please contact Claus Lundegaard






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