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INTERNET TRANSMITTED version of Biological Sequence Analysis - #27803

Information for participants

Go directly to COURSE PROGRAMME

DAILY SCHEDULE
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 16.30 pm.
Discussion from 16.30 - 17.00 pm.

For the afternoon exercises you are supposed to log on to one of CBS' central servers using the User ID and password forwarded to you in an email.
To avoid overloading any single machine,
users 1 - 25 should log on to 'cell.cbs.dtu.dk';
users 26 - 52 should log on to 'organism.cbs.dtu.dk'
- via ssh as described below.

EVALUATION FORMS
Please fill out the evaluation forms daily. Your feedback will help us improve the course. 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.
  • SSH - Secure Shell - from www.ssh.com
    For doing the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
    If you use windows you can download a non-commercial version of ssh by clicking on the link above and do the following:
    • Make a standard install and start the SSH client.
    • Add a new profile - name it CBS.
    • Edit the profile. On the 'Connection' tab use 'genome.cbs.dtu.dk' as host name and your assigned user ID as user name (example: phd33). Compression should be set to 'zlib' and terminal answerback to 'Xterm', press OK.
    • Edit the profile again choose this time the 'Tunneling' tab. Mark the checkbox 'Tunnel X11 connections' and press OK. In case you want to get smart and do both 'Connection' and 'Tunneling' tabs at the same time - don't - it does not work.
    • Save your settings (the floppy).
    • Whenever you want to connect to the CBS server you just start the SSH client and choose the CBS profile and write your password. First time you connect you are asked to accept a server key - just do it.
    If you use unix or Mac OS 10 SSH is (or should be) built into your system and we assume you know your own system, so it will not be covered here.
  • X-Server
    You also need a X-server running to see the unix GUI (grafical interface). Any X-server running on your computer will do. If you don't have one, then we provide one here, which you can use for the duration of the course. Please remember to uninstall the x-server when the course is over.
    The X-server must be running if you want to use X (clustalW, nedit, etc.) on the CBS server.
    We recommend X-win32 and have provided links for installation below.
    Download special X-win32.
    • You need a license when installing this software. Write your password here:
    • Do a standard install using the license.
    • When you run the program then a dialog will pop up. Either cancel the dialog box or fill it out with anything plausible. Filling it out once will stop the dialog from appearing again. The data is not used for anything in this setup, the software just thinks it needs it.
    • When you are running a small blue X will appear in your systray.

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

- Click on the day to open the Breeze Live sessions
- Links to Background Texts are included under the individual days (the links are currently being updated and more will be added as the course proceeds).
- Links to recordings of the day's lectures will be added at the end of the day.

O Monday, May 8

Pair-wise Alignment and Database Searching
Recordings:    Brunak    Gorm    Exercise summary
9.00-9.45
Introduction to bioinformatics and systems biology
Søren Brunak
9.45-10.15
Coffee Break
10.15-12.00
Pairwise sequence alignment and database searching: global and local alignments, substitution matrices, gap penalties, statistical significance
Anders Gorm Pedersen Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: searching databases of nucleotide and amino acid sequences
Anders Gorm Pedersen
16.30-17.00
Discussion

O Tuesday, May 9

Multiple Alignment and Phylogeny
Recordings:    Blom    Gorm I    Gorm II    Gorm III    Exercise
9.00-9.45
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction
Anders Gorm Pedersen Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: multiple alignments, construction of phylogenetic trees
Anders Gorm Pedersen
16.30-17.00
Discussion

O Wednesday, May 10
Immunology and Phylogeny
Recordings:    Lundegaard    Gorm I    Gorm II    Exercise I    Exercise II
9.00-9.45
Immunological bioinformatics
Claus Lundegaard
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny
Anders Gorm Pedersen
Handout (PDF)
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Maximum likelihood phylogeny
Anders Gorm Pedersen and Rodrigo Oliveira
16.30-17.00
Discussion

O Thursday, May 11

Gene Expression and DNA array technology
Recordings:    Friis    Juncker    Workman    Exercise I    Exercise II    Exercise III    Exercise IV
9.00-9.45
Introduction to DNA microarray technology
Carsten Friis  
9.45-10.15
Coffee Break
10.15-11.00
PCA, clustering and classification
Agnieszka S. Juncker
11.15-12:00
Epistasis analysis by microarray data
Chris Workman
12.00-13.00
Lunch Break
13.00-16.30
Exercise: Probe design using OligoWiz 2.0    Lecture Notes
Rasmus Wernersson

Exercise: Classification of array data
Agnieszka S. Juncker
16.30-17.00
Discussion

O Friday, May 12

No class ("Store bededags" holiday).


O Monday, May 15

DNA Structure
Recordings:    Intro    E.coli    Comp.Micro    Exercise I    Exercise II
9.00-9.45
Introduction to Comparative Genomics
David Ussery
9.45-10.15
Coffee Break
10.15-11.00
Chromatin and Gene Expression in E.coli
David Ussery
11.00-11.15
Break
11.15-12.00
Comparative Microbial Genomics
David Ussery
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Comparative Bacterial Genomics
David Ussery
16.30-17.00
Discussion

O Tuesday, May 16

Hidden Markov Models and Gene Finding
Recordings:    Lund    Nikolaj I    Nikolaj II    Intro Exercise
9.00-10.00
Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov Models

Ole Lund
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Handout (PDF) ONLINE PARTICIPANTS: PLEASE PRINT BEFORE LECTURE
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Hidden Markov model and weight matrix construction
Ole Lund
Gene finding in eukaryotes.
Nikolaj Blom
16.30-17.00
Discussion

O Wednesday, May 17

Fold Recognition
Recordings:    Blicher    Lund I    Lund II    Intro Exercise    Questions - Exercise    Exercise Summary
9.00-9.45
Protein Structure
Thomas Blicher
9.45-10.15
Coffee Break
10.15-11.00
Protein Secondary Structure Prediction
Pernille Andersen
11.15-12.00
Fold Recognition
Ole Lund
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Claus Lundegaard and Ole Lund
16.30-17.00
Discussion

O Thursday, May 18

Datadriven Prediction
Recordings:    Brunak I    Brunak II    Brunak III    Intro Exercise    Exercise    Exercise Summary
9.00-10.00
Datadriven prediction methods and neural networks
Søren Brunak
10.00-10.30
Coffee Break
10.30-11.30
Applications: learning from evolution to predict protein structure
Søren Brunak
11.30-12.00
Application: prediction of post-translational modifications and protein function
Søren Brunak
12.00-13.00
Lunch Break
13.00-16.30
Exercises: signal peptide prediction, neural network training, performance measures and evaluation of prediction quality
Søren Brunak
16.30-17.00
Discussion

O Friday, May 19

Protein Modelling and Drug Discovery
Recordings:    Munk Jørgensen    Blicher    Intro Exercise    Exercise Summary    Course Evaluation
  • BACKGROUND TEXTS
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen
09.45-10.15
Coffee Break
10.15-11.00
Computational decision support for drug design. Profilling of small molecule compound libraries
Anne Marie Munk Jørgensen
11.15-12.00
Homology modeling and model evaluation
Thomas Blicher   Lecture notes
12.00-13.00
Lunch Break
13.00-15.00
Exercises: Homology modeling
Thomas N. Petersen, Thomas Blicher
15.00-16.00
Course Evaluation and perspectives for the future





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