Goals

After this course you should be familiar with the most common bioinformatical tools. You should be able to search for a sequence in a database, and you should be able to know something about databases. Most importantly you will know where to look for a tool to anwer your problem the day you need it.

Besides the practical use you should understand how different methods in bioinformatics work. You should be familiar with concepts such as synamic programming, neural networks and Hidden Markov Models. You should be know in how these computational methods can be used on bioscientifically problems and what their limitations are.

Schedule

The course consist of Practical Assignments and stuff to Learn. All practical assignments should be done and submitted individually. All assignments are completely done on the Internet.

Practical Assignment

There is one practical report each week. They are all a requirement for the course. The practical assignments can be done at any time and place during the duration of the course. If you have problems you can ask one of the teachers (AE,RG,EW) preferably by email otherwise by phone (16 1553). If you use the computer lab at KÖL please remember that scheduled events have priority so do not count on using a computer all the time.

Stuff to Learn

For each week there will be a list of questions that you are expected to be able to answer at the exam. For your help to understand the subjects there are lectures, suggested readings and a mandatory weekly seminar. At the seminar you are expected to be able to discuss the different questions from this week. The seminars should not be seen as a exam but as a chance for you to understand the subject better.

Mandatory Events

Besides the seminars and the exam, there are two mandatory events, the introduction and the case study. The introduction is mandatory as we need to set up computer accounts for all of you. Before the case study you should read the paper by Sali et al.

Exam

At the exam you will be given some of the weekly questions and answer them. You are allowed to bring any papers, books etc to the exam.

Scheduled events.

Note this schedule can be changed, check in often. everything marked with a * are mandatory . [Gr1]=Group 1, [Gr2]= Group 2

27/10 09:00-12:00 KÖL, Introduction to the computer tasks. Netscape, ICM and Rasmol (AE,RG,EW)
27/10 13:00-15:00, 4V Databases in Bioinformatics (HM)
28/10 13:00-15:00, 4V Sequence analysis (GvH)
29/10 13:00-15:00, 4V Finding sequences in a database (EW)
30/10 13:00-15:00, 4V Motifs & Signals (HN)
* 31/10 * 10:00-12:00 [Gr2] 5Lunch, 13:00-15:00 [Gr1] 4V Seminare: Sequence searches etc (RG)

3/11 13:00-15:00, 4V Secondary structure predictions. (AE)
4/11 10:00-12:00, C314 Methods for evolutionary studies of genes and genomes (SA)
4/11 13:00-15:00, 4V Sequence families and multiple sequence alignments (AE)
5/11 13:00-15:00, 4V Predicting membrane regions. (BP)
6/11 13:00-15:00, 4V Threading (AE)
* 7/11 * 10:00-12:00 [Gr1] 5Lunch, 13:00-15:00 [Gr2] 4V Seminar: Structure predictions (AE)

10/11 13:00-15:00, 4V Homology Modeling. (AE)
11/11 13:00-15:00, 4V Detecting a wrong structure. (AE)
12/11 12:00-14:00, 4V Protein folding simulations. (AE)
*13/11* 09:00-12:00 C314 Case study of simplified models of protein folding models. To read before excersize: Sali A; Shakhnovich E; Karplus M. "How does a protein fold?". Nature, 1994 May 19, 369(6477):248-51.
13/11 13:00-15:00, 4V Simplified models of protein folding. (AE)
* 14/11 * 9:00-10:30 [Gr1] 5Lunch, 10:30-12:00 [Gr2] 4V Seminar: Protein Folding(AE)
* 14/11 EXTRA ! 13:00-15:004VBioinformatics in genome comparisons.(AL)

17/11 13:00-15:00, P&U Modeling, Drug Design. (MN)
17/11 15:00-16:00 P&U Visit to Pharmacia & UpJohn
18/11 13:00-15:00, 4V More about protein structures. (PN)
19/11 13:00-15:00, 4V Comparing structures, not sequences (AE)
*20/11 * 9:00-10:30 [Gr2] C314, 10:30-12:00 [Gr1] C314 Seminar: Protein Structures(RG)
20/11 13:00-15:00, 4V Modeling, molecular dynamics. (LN)
* 21/11, * 12:00-15:00 in 4V

Teachers

Locations

KöL Computer room K313 in KöL Arrheniuslab, Stockholms University
4V Room 4V at Biochemistry, Arrheniuslab. Stockholms University
P&U Pharmacia & Upjohn,
C314Room C314 in Arrheniuslab
5Lunch Lunch room on 5th floor at Biochemistry, Arrheniuslab. Stockholms University

Arne Elofsson

Last modified: Wed Oct 29 16:32:51 MET 1997