Introduction to bioinformatics - Turbo version - Course program 2011
Introduction to bioinformatics - Turbo version >> Course program 2011
The Technical University of Denmark, Lyngby Campus, Building 208, Room 062. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.
The course runs for the duration of Weeks 23-25 (Mon 6th of June to Fri 24th of June) from 9:15 to ~16:30 (or whenever the computer exercises of the day have been completed). During the first week, we will start each day with lectures in the morning, and conclude with computer exercises in the afternoon. The second and third weeks will be dedicated to group project work.
- Course materials:
The course materials include hand-out notes and the computer exercises themselves. There is no formal textbook. All needed reading material will be available online, linked directly from this page. The material can be read on a day-to-day basis.
Project work will culminate in a poster presentation on Friday, 24 June. Grades will be based on participation (both lectures and exercises) and on the project (poster presentation).
Required hardware / software
The computer exercises can be executed from any internet connected computer (Mac, Linux, Windows) with a modern browser (e.g. Firefox, Safari or Internet Explorer) and Java installed. Java is used in some exercises to run visualization software. Link: www.java.com
We recommend 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. Link: www.pymol.org.
Free Student's version: On Campusnet
If necessary, a username/password will be mailed to you, or provided at the course.
Each group has to keep a "log book" with answers to the questions asked in the exercises. After completing an exercise, upload it via Campusnet under the given day. All exercises have to be handed in on the same day.
The log book should be kept as minimalistic as possible - the important thing here is to focus on giving a nice and simple overview of your answers and not to spend a lot of time on fancy formatting. For example:
Answers to the Multiple Alignment exercise ------------------------------------------ Report by: Rasmus Wernersson (v18103) Question 1 ---------- Fasta format file: >goat_alpha_globin_II ATGGTGCTGTCTGCCGCCGACAAGTCCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCAGCAACGCTGGAG CTTATGGCGCAGAGGCTCTGGAGAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTCCCCCACTT CGACCTGAGCCACGGCTCGGCCCAGGTCAAGGGCCACGGCGAGAAGGTGGCCGCCGCGCTGACCAAAGCG GTGGGCCACCTGGACGACCTGCCCGGTACTCTGTCTGATCTGAGTGACCTGCACGCCCACAAGCTGCGTG TGGACCCGGTCAACTTTAAGCTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTGCCACCACCCCAGTGA TTTCACCCCCGCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAA TACCGTTAA >xxx_yyy_qqq ATAGATAGT .... Question 2 ---------- 2a): xxxx yyyy zzzz 2b): ddd jjj uuu
Please note: We collect these answers for two purposes:
- Assessing participation in the exercises.
- As a means to improve our teaching, since we get a chance to learn what questions are typically difficult to answer or understand.
Lecture Plan 2011
Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!
Monday 6 June
- Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
- Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
- Lecture 3 - Proteins - data and databases - Henrik Nielsen.
Tuesday 7 June
- Lecture 1 - Pairwise alignment - Anders Gorm Pedersen
- Page 35-55 in Immunological Bioinformatics (PDF - extract from the Book - password protected)
- Handout exercise:
- Lecture 2 - Introduction to BLAST - Anders Gorm Pedersen
Wednesday 8 June
- Lecture 1 - Multiple alignment - Anders Gorm Pedersen
- Slides: PDF
- Exercise: Multiple alignment (Exercise helper: Oksana Lukjancenko)
- Lecture 2 - Phylogenetic trees - Anders Gorm Pedersen
- Handout exercise: Reconstruction of a distance tree
- Slides: PDF
- Exercise: Phylogenetic trees (Exercise helper: Oksana Lukjancenko)
- Lecture 3 - Protein 3D structure - Thomas Blicher
Thursday 9 June
- Lecture 1 - PSI-BLAST - Morten Nielsen
- Page 68-80 in Immunological Bioinformatics (PDF - extract from the Book - password protected)
- Lecture 2 - Prediction methods in immunological bioinformatics - Ole Lund & Morten Nielsen
- Modeling the adaptive immune system: predictions and simulations
- Page 91-102 in Immunological Bioinformatics (PDF - extract from the Book - password protected) (The Neural Network equations will not be essential, and are not covered in detail).
Friday 10 June
- Lecture 1 - From DNA to portrait - H. Bjørn Nielsen
- 9.45 -10.15: Introduction to projects - Aron Charles Eklund and project leaders.
- Exercise 1: (Exercise helper Agata Wesolowska)
- Lecture 2 - Human Genome Browser - Thomas Nordahl Petersen
Monday 13 June
- DTU holiday; no class today.
Tuesday 14 June – Thursday 23 June
- Work in groups on projects.
Friday 24 June
- Poster session and examination.
Groups of 3-5 individuals will form a project team. The following four projects are available, with separate project leaders. Project preferences will be collected, and projects will be allocated, with an attempt to match preferences.
Group list: 27622 Project Groups 2011
Project 1 - Genomic epidemiology and the Haiti cholera outbreak - (Simon Rasmussen)
- The introduction of second generation sequencing and the capabilities to sequence hundreds of bacterial strains simultaneously is about to transform our ability to track and study outbreaks of pathogenic bacteria – also known as epidemiology. In the project you will try to investigate an outbreak of Vibrio cholerae that followed the 7.0 (Richter scale) earthquake that struck Haiti on 12th January 2010. The earthquake destroyed a large part of the capital Port-au-Prince and the surrounding area making 1.5 million people homeless and killing between 50,000 - 300,000. The following breakdown of sanitation and clean water supply lead to a cholera epidemic outbreak in October 2010 from which more than 100,000 were affected and 3,300 died, this at a rate of 50 per day. Because cholera epidemics had not been seen in Haiti before, the outbreak was claimed to be introduced by foreign help workers which lead to both diplomatic tension and civil unrest. Here you will try to combine the use of Illumina and Pacific Bioscience sequence data, massive parallel genome assembly and SNP identification to identify the geographical source of the outbreak.
Project 2 - Non-synonymous mutations and cancer (Aron Eklund)
- Cancer is a genetic disease in which the tumor cell's genome is altered relative to the patient's normal genome. Several genes are frequently found mutated in cancer, suggesting that the mutation may change the gene's function to give the tumor cell a selective advantage. This project involves analysis of tumor-associated gene mutations in order to understand how the mutation causes or enables cancer development.
Project 3 - Polymorphism of human cytochrome P450 enzymes and their roles in drugs efficacy and adverse effects (Olivier Taboureau)
- A study of how interindividual variations in the DNA sequence of cytochrome P450 enzymes (CYPs) affect drug response. The human CYP super family contains 57 functional genes and 58 pseudogenes playing an important role in the metabolism of therapeutic drugs, xenobiotics and endogenous compounds. Based on the sequences of the 57 functional genes, the team should develop a multiple sequence alignment and a phylogenetic tree. By integrating information from several bioinformatics and chemoinformatics web resources, the effect of Single Nucleotides Polymorphisms (SNP) on efficacy and adverse effects of drugs will be studied.
Project 4 - Immunological bioinformatics (Ole Lund)
- The immune system normally does a good job of keeping us free from diseases, but sometimes it fails. One approach towards understanding why this happens is to produce advanced simulation models of the immune system and to understand the relationship between hosts and patogens in this manner. Depending on the complexity of these models and the input given, they can be used to simulate what happens when a host gets infected by a pathogen, thereby predicting the co-evolvement of pathogens and immune systems. One aim of the modeling is to identify parts of proteins known as epitopes which are recognized by the immune system, thereby inducing a protective response. This knowledge is very valuable in the development of better vaccines and provides very important insights into the nature of cancer, allergy and autoimmune diseases.