|
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.
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
Monday, June 8
Introduction and immunology brush up
- BACKGROUND TEXTS: Chapters 12;
- 9.00 - 9.20
- Introduction to the course.
- Claus Lundegaard, CBS.
- 9:20-10:15
- Basic mechanisms of immune defense, Lisbeth Nielsen Fink, CBS.
- 10.15 - 10.45
- Coffee Break
- 10.45 - 12.00
- Basic mechanisms of immune defense, Lisbeth Nielsen Fink, CBS
- 12.00 - 13.00
- lunch break
- 13.00 - 15.30
- Exercises: Databases and web resources in Immunological bioinformatics.
Claus Lundegaard, CBS.
Tuesday, June 9
Pathogens, vaccines and antibodies
- BACKGROUND TEXTS:
Chapters 2, 10-11.
- 9.00 - 9.15
- Yesterdays exercise round up
- 9.15 - 10.00
- Challenges to the Immune System PowerPoint Slides
Ole Lund, CBS
- 10.00 - 10.30
- Coffee Break
- 10.30 - 11.15
- Vaccines and epitope dicovery.
- Claus Lundegaard, CBS
- 11.15 - 12.00
- Antibodies and TCRs, development and selection.
Claus Lundegaard, CBS.
- 12.00 - 13.00
- lunch break
- 13.00 - 15.30
- Exercises:
- Inroduction to the Exercise.
- Analysis of immunoglobolin gene rearrangements.
Claus Lundegaard, CBS.
Wednesday, June 10
T-cell Epitopes
- 9.00 - 9.15
- Yesterdays exercise round up
- 9.15 - 10.00
- Training and evaluation of predictive methods.
- Claus Lundegaard, CBS.
- Handout
- 10.00 - 10.30
- Coffee Break
- 10.30 - 11.30
- Prediction of MHC peptide binding.
Claus Lundegaard, CBS.
- 11.30 - 12.00
- Prediction of proteasome processing and TAP binding; The Class I Pathway.
- Handout.
Claus Lundegaard, CBS.
- 12.00 - 13.00
- Lunch Break
- 13.00 - 16.30
- Exercise:
- Prediction Training Exercise.
- Claus Lundegaard, CBS
Thursday, June 11
Supertypes, HLA clustering, and pan-predictions
- 9.00 - 9.15
- Yesterdays exercise round up + Answers.
- 9.15 - 10.00
- Supertypes and Clustering
- Claus Lundegaard, CBS
- 10.00 - 10.30
- Pan-specific predictors.
- Claus Lundegaard, CBS.
- 10.30 - 11.00
- Coffee Break
- 11.00 - 11.30
- Integration of predictions
Thomas Strantzl, CBS.
- 11.30 - 12.00
- Prediction of Sars binders and Pox CTL epitopes.
- Claus Lundegaard, CBS.
- 12.00 - 13.00
- Lunch Break
- 13.00 - 17.00
- Exercises:
- Proteasome and TAP predictions
Claus Lundegaard + Thomas Strantzl, CBS.
- Unix Crash Course
Claus Lundegaard, CBS.
Friday, June 12
Structures, Homology modeling, and B cell epitope predictions
- 9.00 - 9.15
- Yesterdays exercise round up.
- 9.15 - 10.00
- Protein structures and homology modelling
Ole Lund, CBS.
- 10.00 - 10.30
- Coffee Break
- 10.30 - 11.15
- Prediction of B cell epitopes
Claus Lundegaard, CBS.
- 11.15 - 12.00
- Exercise: B cell epitope predictions.
Claus Lundegaard + Bent Petersen, CBS.
- 12.00 - 13.00
- Lunch Break
- 13.00 - 15.30
- Exercise: B cell epitope predictions continued.
Claus Lundegaard + Bent Petersen, CBS.
Monday, June 15
Evolution of the immune system and viral pathogens
- BACKGROUND TEXTS: Chapter 3
- 9.00 - 9.15
- Friday's exercise round up.
- 9.15 - 10.00
- Recent discoveries on evolution of immune systems.
- Claus Lundegaard, CBS.
- 10.00 - 10.30
- Coffee Break
- 10.30 - 12.00
- Molecular Evolution. Handout exercise
Anders Gorm Pedersen, CBS.
- 12.00 - 13.00
- Lunch Break
- 13.00 - 16.00
- Exercises: Viral Evolution
Anders Gorm Pedersen and Claus Lundegaard, CBS.
Tuesday, June 16
Populations and simulations
- 9.00 - 9.15
- Yesterday's exercise round up
- 9.15 - 10.00
- Pathogen diversity, Flu and HIV.
- Claus Lundegaard, CBS.
- 10.15 - 10.45
- Coffee Break
- 10.45 - 11.15
- HLA frequencies and population diversities.
Claus Lundegaard, CBS.
- 11.15 - 12.00
- Mathematical simulations of HIV infections
Nicolas Rapin, University of Copenhagen, Faculty of Pharmacy.
- 12.00 - 13.00
- Lunch Break
- 13.00 - 15.30
- Exercises: Development of vaccines against HCV.
- Claus Lundegaard, CBS.
Wednesday, June 17
Symposium with invited speakers
- 9.15 - 10.00
- Malaria pathogenesis and immunity - a variant-specific perspective
- Lars Hviid, Centre for Medical Parasitology, CSS
- 10.00-10.30
- Coffee Break
- 10.30 - 11.15
- TBA
- Björn Peters, La Jolla Institute for Allergy and Immunology.
- 11.15 - 12.00
- Evolution of resistance in HIV-1 patients based sequence information.
- Søren Banke, Statens Seruminstitut
- 12.00 - 13.00
- Lunch Break
- 13.00 - 13.45
- TB epitope discovery
- Sheila Tang, CBS
- 13.45-14.00
- Coffee Break
- 14.00 - 14.45
- DNA vaccines and HIV-1
- Lasse Vinner, Statens Seruminstitut
- 14.45 - 15.30
- Epitope grafting and antibody engineering - the molecular basis of the allergic reaction
- Kaare Lund, ALK-Abello A/S
Thursday, June 18
Initiation of projects work
- 9.00 - 9.15
- Roundup of exercise from Tuesday.
- 9.15 - 10.00
- Introduction to project work
As Slides
Claus Lundegaard
Monday, June 22
Quiz and exercise exam
- 9.00 - 13.00
- Quiz and exercize exam.
Friday, June 19 to Thursday, June 25:
Project work
Friday, June 26: Poster Presentations and round up
It is possible to do projects of different sizes within the area of immunological bioinformatics.
If you have interest please look at this document for inspiration or contact Claus Lundegaard for special requests.
For more information, please contact Claus Lundegaard. |
Go to
|
