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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 a previous mail.
To avoid overloading any single machine,
users 1 - 12 should log on to 'cell.cbs.dtu.dk';
users 13 - 25 should log on to 'organism.cbs.dtu.dk'
- via ssh as described below.

EVALUATION FORMS
STATUS
The Bulletin Board - YaBB is now up and running at http://www.cbs.dtu.dk/cgi-bin/yabb/YaBB.cgi.
You need to register the first time you go in there. When you've registered, you will receive an email confirmation including a password.

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
- Click on the day to open the Breeze Live sessions

- Links to recordings of the day's lectures will be added around lunchtime

O Monday, April 4

Pair-wise Alignment and Database Searching
Recordings:    Brunak    Gorm I    Gorm II (handout)    Gorm III    Exercise summary
9.00-9.45
Introduction to bioinformatics with focus on the human, mouse and rat genomes
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)   Lecture notes
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, April 5

Hidden Markov Models and Gene Finding
Recordings:    Morten Nielsen    Nikolaj I (first 6 slides)    Nikolaj II    Nikolaj III
   Exercise summary - Morten Nielsen    Exercise summary - Nikolaj
9.00-10.00
Finding sequence motifs: consensus sequences, weight matrices, information content,
sequence logos, and Hidden Markov Models
Morten Nielsen   Lecture notes   Article
10.00-10.30
Coffee Break
10.30-12.00
Eukaryotic gene finding
Nikolaj Blom   Handout (PDF)   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises:
Hidden Markov model and weight matrix construction
Morten Nielsen
Gene finding in eukaryotes.
Nikolaj Blom
16.30-17.00
Discussion

O Wednesday, April 6

Multiple Alignment and Phylogeny
Recordings:    Nikolaj Blom    Gorm - Mult.Align.    Gorm - Phylogeny I    Gorm - Phylogeny II    Exercise summary - Gorm
9.00-9.45
Resources of biomolecular data: sequences, structures and functionality - with emphasis on the human genome
Nikolaj Blom   Lecture notes
9.45-10.15
Coffee Break
10.15-12.00
Multiple alignment and phylogenetic reconstruction
Anders Gorm Pedersen Handout (PDF)   Lecture notes
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 Thursday, April 7

Immunology and Phylogeny
Recordings:    Ole Lund - Immunology    Gorm - Max.Like I    Gorm - Max.Like II
   Introduction to Exercise - Gorm    Exercise summary - Gorm
9.00-9.45
Immunological bioinformatics
Ole Lund  Lecture notes
9.45-10.15
Coffee Break
10.15-12.00
Maximum likelihood phylogeny
Anders Gorm Pedersen   Handout (PDF)   Lecture notes
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 Friday, April 8

Datadriven Prediction
Recordings:     Brunak I     Brunak II I     Brunak III
    Brunak - Introduction to exercises     Brunak - Exercises summary
9.00-10.00
Datadriven prediction methods and neural networks
Søren Brunak   Lecture notes
10.00-10.30
Coffee Break
10.30-11.30
Applications: learning from evolution to predict protein structure
Søren Brunak   Lecture notes
11.30-12.00
Application: prediction of post-translational modifications and protein function
Søren Brunak   Lecture notes
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 Monday, April 11

Fold Recognition
Recordings:     Anne Mølgaard I     Morten Nielsen; Anne Mølgaard II     Introduction to exercises     Exercise summary
9.00-10.00
Protein Structure
Anne Mølgaard   Lecture notes
10.00-10.30
Coffee Break
10.30-11.15
Fold Recognition
Morten Nielsen   Lecture notes
11.15-12.00
Homology modeling and model evaluation
Anne Mølgaard   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Fold recognition using web servers
Claus Lundegaard and Morten Nielsen
16.30-17.00
Discussion

O Tuesday, April 12

Protein Modelling and Drug Discovery
Recordings:     Thomas Nordahl, MySQL     Anne Marie Munk Jørgensen     Pernille Andersen
    Exercise introduction     Exercise summary
9.00-09.45
Gene Discovery by use of MySQL
Thomas Nordahl Petersen   Lecture notes
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   Lecture notes
11.00-12.00
Protein Secondary Structure: Classification and Prediction
Pernille Andersen   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30
Exercises: Homology modeling
Thomas N. Petersen, Anne Mølgaard
16.30-17.00
Discussion

O Wednesday, April 13

DNA Arrays
Recordings:     Knudsen I     Knudsen II     Tommerup
    Exercise introduction     Exercise summary
9.00-9.45
Introduction to DNA microarray technology
Steen Knudsen   Lecture notes (Chapter 1-3)
9.45-10.15
Coffee Break
10.15-11.00
Normalisation and significance of array data
Steen Knudsen   Lecture notes (Chapter 4)
11.00-12.00
Developmental disorders and gene expression
Niels Tommerup   Lecture notes
12.00-13.00
Lunch Break
13.00-16.30 Exercises:
13.00 GenePublisher
Steen Knudsen
14.00 Probe design using OligoWiz 2.0 (Exercise introduction)
Rasmus Wernersson   Exercise guide   OligoWiz 2.0 server
16.30-17.00
Discussion

O Thursday, April 14

Gene Expression and DNA array technology
Recordings:     Knudsen I     Knudsen II     Ulrik de Lichtenberg
    Exercise introduction     Exercise summary I     Exercise summary II
9.00-10.00
PCA, clustering and classification (Chapter 5, 6, 10)
Steen Knudsen   Lecture notes
10.00-10.30
Coffee Break
10.30-11.15
Promoter analysis, pathway analysis and inference of regulatory networks (Chapter 7, 8, 9)
Steen Knudsen
11.15-12:00
Case story: Using Microarrays to Study Cell Cycle Regulation
Ulrik de Lichtenberg Lecture notes
12.00-13.00
Lunch Break
13.00-16.00
Exercises:
Classification of array data
Inferring regulatory networks
Steen Knudsen
16.30-17.00
Discussion

O Friday, April 15

DNA Structure
Recordings:     Ussery I     Ussery II     Ussery III
    Exercise introduction     Exercise summary     Evaluation
9.00-9.45
Introduction to Comparative Genomics
David Ussery   Lecture notes
9.45-10.15
Coffee Break
10.15-11.00
Chromatin and Gene Expression in E.coli
David Ussery   Lecture notes
11.00-11.15
Break
11.15-12.00
Comparative Microbial Genomics
David Ussery   Lecture notes
12.00-13.00
Lunch Break
13.00-15.00
Exercises: Comparative Bacterial Genomics
David Ussery
15.00-17.00
Course Evaluation and perspectives for the future





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