Introduction to bioinformatics - Turbo version - Course program 2012
Introduction to bioinformatics - Turbo version >> Course program 2012
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 from Friday the 1st of June to Friday the 22nd of June, from 9:15 to ~16:30 (or whenever the computer exercises of the day have been completed). There will be no class on June 5 (Constitution Day). 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, 22 June. Grades will be based on 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.
Working in groups is allowed. Each group has to keep a text document with answers to the questions asked in the exercises. After completing an exercise, upload it via Campusnet under the given day. Remember to state the members of the group so everyone can get credited; one submission per group is enough. All exercises have to be handed in on the day when it was assigned. Late exercises will receive half credit.
The submitted document 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
Lecture Plan 2012
Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!
Friday 1 June
- Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
- Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
- Slides (PDF):
- Lecture 3 - Proteins - data and databases - Henrik Nielsen.
- Slides (PDF):
- Exercises - (Exercise helper: Asli Ozen)
Monday 4 June
- Lecture 1 - Pairwise alignment - Rasmus Wernersson
- Page 35-55 in Immunological Bioinformatics (PDF - extract from the Book - on Campusnet in the folder "Reading materials")
- Handout exercise:
Tuesday 5 June
Constitution Day -- no class.
Wednesday 6 June
NOTE! Class will be in Building 306 room 96
- Lecture 1 - Multiple alignment - Anders Gorm Pedersen
- Slides: PDF
- Exercise: Multiple alignment (Exercise helper: Francesco Favero) - (Answers )
- Lecture 2 - Phylogenetic trees - Anders Gorm Pedersen
- Handout exercise: Reconstruction of a distance tree
- Slides: PDF
- Exercise: Phylogenetic trees (Exercise helper: Francesco Favero) - (Answers)
- Lecture 3 - Protein 3D structure - Thomas Blicher
- Exercises: (Exercise helper: Francesco Favero)
Thursday 7 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 - 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).
- Exercises: (Exercise helper Salvatore Cosentino)
Friday 8 June
- 9.15 - 9.45: Special lecture - MetaGenomic Species - learning structure from metagenomics - H. Bjørn Nielsen
- 9.45 -10.15: Introduction to projects - Aron Charles Eklund and project leaders.
- Lecture 1 - Functional Human Variation Agata Wesolowska
- Lecture 2 - Human Genome Browser - Thomas Nordahl Petersen
- Exercise 2 (Exercise helper Josef Korbinian Vogt)
- Exercise 2 (answers)
Monday 11 June – Thursday 21 June
- Work in groups on projects.
- Posters (as a PDF file) must be submitted to CampusNet by 12:00 noon on Thursday, 21 June.
Friday 22 June
- 09:15 - Poster session and oral examination inside the main entrance to building 208 (upstairs from the classroom).
Groups of 3-5 individuals will form a project team. The following three projects are available, with separate project leaders. Project preferences will be collected, and projects will be allocated, with an attempt to match preferences.
NOTE: Projects are subject to change.
Project 1 - 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 2 - 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 3 - Immunological bioinformatics (Morten Nielsen)
- 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.