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

Bioinformatik: It og Sundhed - course programme, winter 2009


Teachers:

Curriculum:
The curriculum consists of hand-out notes and the computer exercises themselves. There is no formal text-book. All needed reading material will be available online, linked directly from this page. The material can be read on a day-to-day basis.

Exam:
Oral exam 7-scale grades.

Where and when:
The Technical University of Denmark, Lyngby Campus, Exact location at DTU-CBS (Building & room) to be announced later. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions. Map of the DTU buildings here.

The course runs for 10 weeks with lectures and exercises 1 day a week (week 46 - week 3) from 9:15 to ~16:00 (or wheneven the computer execersis of the day has been completed).
The exam will be in week 4, 2010.
Each day starts with lectures in the morning, and concludes with computer excersices in the afternoon. Teaching will be in danish, but slides and readings are most often in english.


Hardware / Software used

The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. FireFox, Safari or a recent version of Internet Explorer - a browser which supports tabs is recommended) and Java installed. Java is used in some exercises to run visualization software. Link: www.java.com.

We recomment the JEdit text editor for use on sequence files, since it is well suited for this purpose and is platform independent. Link: www.jedit.org.

For the protein structure exercise the PyMOL software (also cross-platform) will be used. Main link: www.pymol.org.

Free Student's version:

Username/password will be mailed to your all by Thomas Blicher

Useful links:

Collection of links: show me

Course programme:

Week 46 - Thursday 12th of November

Lecture 1: Introduction to the course - Build 208, room 60 - Thomas Nordahl Petersen
Slides: Introduction

Lecture 2: Biological information, DNA structure and sequencing, GenBank searching - Build 208, room 60 - Rasmus Wernersson

Readings: GenBank (The yearly GenBank publication, 2008). DNA sequencing tutorial - source: IDT Tech Vault.
Slides: Biological information + DNA data
Hand outs: Chromatogram - GenBank + FASTA format.

Lecture 3: Amino Acids and Proteins - Build 208, room 60 - Thomas Nordahl Petersen
Slides: Amino acids and proteins

Exercises, Build 208, Room 027 the library
1) Searching the GenBank.
2) Protein Databases.


Week 47 - Monday 16th of November

Lecture 1: General biological introduction - Build 208, room 027 Library - Lisbeth Nielsen Fink
Slides: Generel biologisk introduktion
Hand outs: Quiz

Lecture 2: Evolution and DNA - Build 208, room 027 Library -

Reading:Brief introduction to evolutionary theory - Anders Gorm Pedersen
Slides: Evolution intro
pdf: Evolution intro


Exercises moved to next week


Week 48 - Monday 23th of November

Lecture 1: Substitution matrices and Log-odds scores - Build 208, room 62 - Thomas Nordahl Petersen Slides: ppt
Readings for lecture 1 and 2: p. 35-47

Lecture 2: Global and local alignment - Build 208, room 62 - Thomas Nordahl Petersen Slides: ppt

Exercises, Build 208, Room 027 the library
1) Sequence alignment the hard way - on paper - Thomas Nordahl Petersen
Exercise: pdf

Exercises, Build 208, Room 027 the library
2) Pairwise alignment


Week 49 - Thursday 3th of December

Lecture 1: Introduction to Blast - Build 208, room 60 - Thomas Nordahl Petersen
Slides: BLAST powerpoints
Handouts: BLOSUM62 matrix - BLASTN heuristics - BLASTP heuristics.

Lecture 2: Psi-Blast - Iterative Blast searches and Position Specific Scoring Matrices - Build 208, room 60 - Bent Petersen
Slides: PowerPoint slides.

Readings: Page 68-80 in Immunological Bioinformatics (PDF - extract from the Book - password protected)

Exercises, Build 208, Room 027 the library
1) Using BLAST for sequence searches - Thomas Nordahl Petersen


Week 50 - Thursday 10th of December

Lecture 1: Mutiple alignments - Build 208, room 60 - Rasmus wernersson
Slides: PowerPoint slides.
Readings: Mutiple Sequence Alignment (Short software review paper)
Readings:RevTrans (Short paper on an apporach which mixes DNA and protein alignment)

Lecture 2: Phylogenetic trees - Build 208, room 60 - Anders Gorm Pedersen
Slides: PowerPoint slides.
Readings: Introduction to Treebuilding (PDF) - Evolutionary trees (except the section "How to reconstruct an evolutionary tree").
Hand-outs: handout exercise Reconstruction of a distance tree

Exercises, Build 208, room 60
1) Mutiple alignments and phylogenetic trees


Week 51 - Tuesday 15th of December

Lecture 1: title - Build 208, room 60 - Ramneek Gupta

Lecture 2: Genome Browsers - Build 208, room 60 - Thomas Nordahl Petersen
Readings:UCSC Genome Browser, Update 2008 Slides: PowerPoint slides



Exercises, Build 208, room 60
1) Using the UCSC genome browser - Thomas Nordahl Petersen
2) exercise (announced later) - Ramneek Gupta


Week 51 - Thursday 17th of December

Lecture 1: Protein 3D-structure - Build 208, room 60 - Thomas Blicher
Readings: Protein Structure (Wikipedia - Frozen version).
Link to "Live" version: http://en.wikipedia.org/wiki/Protein_structure
Slides: Protein structure

Lecture 2: Homology modelling - Build 208, room 60 - Thomas Blicher
Slides; Homology modelling

Exercises, Build 208, room 60
1) PDB and PyMOL - Thomas Blicher


Week 1 - Thursday 7th of January

Lecture 1: PDB structure - Thomas Blicher Room 060 9:15-10
Slides: PowerPoint

Lecture 2: Introduction to neural networks - Thomas Nordahl Petersen Room 027 Library
Slides: PowerPoint

Lecture 3: Sequence based predictors. Secondary structure and surface accessibility - Bent Petersen Room 027 Library
Slides: PowerPoint pdf Keynote

Exercises
1) SignalP, NetSurfP and Propepdide predictions - Thomas Nordahl Room 027 Library
exercise


Week 2 - Thursday 14th of January All day in: Build 208, Room 027 the library

Lecture 1: Entropy, Information Content & logo plots - Thomas Nordahl Petersen
Readings Page 69-80 in chapter 4:pdf
Readings:WebLogo
Slides: PowerPoint
Handout:Example how to calculate frequencies and make Logo

Lecture 2: Summary - Thomas Nordahl Petersen
Slides: PowerPoint

Exercises
1) Logo plots - Thomas Nordahl Petersen
exercise


Week 3 - Thursday 21th of January All day in: Build 208, Room 027 the library
Example of a written exam. Answer the questions and keep relevate browser windows open.

exercise


Week 4 - Thursday 28th of January

Oral Exam room 027 'The Library' from 9-12



Nedenunder er 5 spørgsmål som først vil kunne læses efter I har trukket et spørgsmål til eksamen.
I får 25 min til forberedelse og 20 min til den mundtlige eksamen. Spørgsmålene er udgangspunkt for det I skal tale om til eksamen.


Spørgsmål 1

Spørgsmål 2

Spørgsmål 3

Spørgsmål 4

Spørgsmål 5

Dette er en test - kan du læse denne pdf