Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

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 306 room 99 (1st floor, isn the databar)
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 Friday, June 1
Introduction, immunology brush up, and Unix
9.00 - 9.30
Introduction to the course.
Ole Lund, CBS, DTU Systems Biology.
9:30-10:15
Basic mechanisms of immune defense
Susanne Brix Pedersen, CBS, DTU Systems Biology.
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
Introduction to Immunological Bioinformatics.
Ole Lund, CBS, DTU Systems Biology.
13.30 - 16.00
Exercises: Unix and awk, a crash course
Ole Lund, CBS, DTU Systems Biology.

O Monday, June 4
Vaccines, antibodies, and epitopes
  • BACKGROUND TEXTS:   Chapters 2, 10. Article1
9.00 - 9.30
Yesterday's exercise round up
Yesterday's exercise round up
9.30 - 10.15
Adjuvants
Prof. Peter Heggaard, DTU-Vet
10.45 - 11.15
Antibodies and TCRs, development and selection.
Ole Lund, 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.
Ole Lund, CBS, DTU Systems Biology.
 
Analysis of immunoglobolin gene rearrangements.
Oler Lund, CBS, DTU Systems Biology.

O Wednsday, June 6
T-cell Epitopes
9.00 - 9.30
Yesterday's exercise 2 part 1 round up
Yesterday's exercise 2 part 2 round up
Exercise 2 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
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.
NN handout.
Morten Nielsen, CBS, DTU Systems Biology.
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 Thursday June 7
B cell epitope predictions
9.00 - 9.30
Exercise round up
Yesterdays exercise round up
Ole Lund, Center for Biological Sequence Analysis, DTU Systems Biology.
9.30 - 10.00
Prediction of B cell epitopes
Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
Recording
10.00 - 12.00
Exercise: B cell epitope predictions.
Jens Kringelum, Center for Biological Sequence Analysis, 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
14.00 - 14.30
Analysis of FACS data using R
Juliet Wairimu Fredriksen, Master student, CBS, Department of Systems Biology, DTU
14.45-
Introduction to project work
Ole Lund, Center for Biological Sequence Analysis, DTU Systems Biology.
Introduction to project work
Poster Guide
Training and evaluation of predictive methods.
Handout

O Friday, June 8
Supertypes, HLA clustering, and vaccine design

9.00 - 9.30
Exercise round up
9.30 - 10.00
Supertypes and functional clustering of MHC molecules
Morten, CBS, DTU Systems Biology.
10.00 - 10.30
What defines a T cel epitope? Is there any thing beyond MHC binding?
10.30 - 10.45
Coffee Break
10.45 - 11.25
Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design
Morten Nielsen, CBS, DTU Systems Biology.
11.25 - 12.00
Identifying multiple sequence motifs in large scale peptide data sets
Massimo Adreatta, CBS, DTU Systems Biology.
Ole Lund, CBS, DTU Systems Biology.
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercises: Development of vaccines against HCV.
Answers
Morten Nielsen, CBS, DTU Systems Biology.

O Monday, June 11
Evolution and viral pathogens
  • BACKGROUND TEXTS:  Chapter 3
9.00 - 9.30
Exercise round up
Yesterdays exercise round up.
NetMHCpan sheet
NetMHCIIpan sheet
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.
12.00 - 13.00
Lunch Break
13.00 - 16.00
Exercises: Viral Evolution
Anders Gorm Pedersen and Ole Lund, CBS, DTU Systems Biology.

O Tuesday, June 12 to Monday, June 18:
Project work
Monday 12.00
Deadline for sending poster ppt/pdf file to lund@cbs.dtu.dk

O Tuesday, June 19
9.00 - 17.00
Poster presentations

O Wednesday-Thursday, June 20-21
9.00 - 17.00
Exam.

O Friday, June 22
Special guest speaker
10.00 - 11.00
Guest speaker
11.00 - 12.00
Course round-up and goodbye


For more information, please contact Ole Lund






Go to