Course27633 >> Course program 2011
The Technical University of Denmark, Lyngby Campus, Building 208, Room 062 (in the basement) in 2011. Teaching in Janurary 2012 will be in other rooms - see info for the teaching on the individual days. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.
The course runs every Thursday (Nov 10'th 2011 - Jan 26'th 2012 from 9:15 to 16 (or whenever the computer exercises of the day have been completed). Each day will start with lectures in the morning, and conclude with computer exercises in the afternoon starting normally at 13:00.
- Course materials:
The course materials include hand-out notes and the computer exercises themselves, which are relevant for the exam. Also, we will use supplementary information from the text book: Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0 which will be available in the DTU bookstore building 101.
Thursday Jan 26'th a 4 hour written exam from 9-13 - bring your own computer and whatever notes you want to use. Exam in room 042+048 in building 210.
In case there is a need for a re-exam it will be Feb 27 2012 (but I hope this will not be an issue). A re-exam is for those of you that might get sick at the ordinary exam day or if you do not pass the course.
- Course description:
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 free and well suited for this purpose and is platform independent. Link: www.jedit.org. You may also choose to use word that you provide yourself. In principle OpenOffice is ok, but we prefere that you use something else or at least save documents in word format.
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.
It is very important that you get custom/familiar with the reporting system as that is what we will use for the written exam in the end of the course.
After completing an exercise, upload it via Campusnet under the given day.
Make sure that the file that you upload has the correct format last name like .doc or .docx for word documents or .txt for simple text files and first name should be your student number and fi more files are uploaded then a period followed by any user text - examples could be:
The answers 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. Minimalistic is good, but still avoiding to give too short answers like:
Answer: yes (rather 'yes' because of ...) Answer: 42 (rather explain how you got that number)
Write your name and study number in the top of every file For example:
Answers to the Multiple Alignment exercise ------------------------------------------ Report by: jens jensen (v18103)
As mentioned before jedit is a suitable text editor - download it here: jedit
Collection of links
- DNA and Amino acids
- Substitition matrices
- Alignment tools
Lecture Plan 2011 - 2012
Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!
Thursday November 10
- Lecture 1 - Introduction to the course - Thomas Nordahl Petersen
- Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
- Lecture 3 - DNA, Amino Acids and Proteins - Thomas Nordahl Petersen.
- page 1-26 (top of p 26) in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Exercises - Henrik Nielsen. (Exercise helper: Bent Petersen.)
Thursday November 17
- Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
- Lecture 2 - Amino acids & proteins part II - Thomas Nordahl Petersen
- page 41-47 (top of p 26) in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Exercises: Thomas Nordahl Petersen
- Learning amino acid properties by use of modeling kit - modeling by hand
Thursday November 24
- Lecture 1 - Substitution matrices and Log-odds scores - Thomas Nordahl Petersen
- Readings for lecture 1 and 2:
- Slides: ppt
- Lecture 2 - Global and local alignment - Thomas Nordahl Petersen
- Readings: for lecture 1 and 2
- Slides: ppt
Thursday December 1
- Lecture 1 - Introduction to Blast - Thomas Nordahl Petersen
- page 165-169 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
- Lecture 2 - Psi-Blast - Iterative Blast searches and Position Specific Scoring Matrices - Bent Petersen
- page 165-169 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0 (same as lecture 1).
Thursday December 8
- Exercise 1
- Extra material:
- Fun multiple alignment "game": Phylo
- Lecture 2 - Pylogenetic trees - Anders Gorm
- handout exercise Reconstruction of a distance tree
Thursday December 15
- Lecture 1 - Protein 3D-structure - Thomas Blicher
- page 95-100 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0. (Some background but Not exam material)
- page 109-111 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0. Relevant for exam.
- Lecture 2 Homology modeling - Thomas Blicher
- page 165-167 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
Thursday January 5 Room 162 Building 210
- Lecture 1 - Genome Browsers - Thomas Nordahl Petersen
Thursday January 12 - room 162 building 210
Thursday January 19 - room 018 building 210
- Lecture 1 - Entropy, Information Content & logo plots - Thomas Nordahl Petersen
- page 170-172 in book Introduction to protein science by Arthur M. Lesk, ISBN:978-0-19-954130-0.
Thursday January 26, room 042+048, building 210
- 4 hour written exam from 9-13
- Building 210 - Room 042+048
- Bring computer and any books you want
- I recommend you bring a mouse, in case you need to work with PyMol, but your touchpad may work for you (no guarantee)
- Link to exam word-document once exam has started
- Link to exam pdf-document once exam has started
- Link to exam word97-dokument once exam has started
Monday February 27 - re-eksamen (mundtlig), room 062, building 208
Du skal møde op i rum 062 og trække et spørgsmål, herefter får du forberedelse som foregår i rum 027, hvor censor eller jeg lige følger dig på plads.
Eksamen foregår ved at du trækker et spørgsmål, som indeholder en mindre praktisk opgave inden for pensum. Du vil så få 30 minutters forberedelsestid, hvor du skal løse den opgivne opgave ved hjælp af din computer. Du vil have adgang til DTU's trådløse internet. Lad alle relevante vinduer være åbne, så du bagefter kan vise, hvad du har gjort. Eksaminationen vil derefter vare ca. 20 minutter og tage udgangspunkt i din egen fremlæggelse af hvordan du har løst opgaven. Der kan dog også forekomme spørgsmål i andre dele af pensum. Karakteren vil blive givet umiddelbart efter din eksamen.
I får en mail fra mig om hvilket tidspunkt I hver især skal møde op til.