Course27633autumn2012

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Course27633 >> Course program 2012

Contents

General information

Where:

The Technical University of Denmark, Lyngby Campus, Building 306, Room 38. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.

When:

The course runs every Thursday (Nov 15'th 2012 - Jan 17'th 2013 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.


Exam:

Monday Jan 21'th a 4 hour written exam from 9-13 - bring your own computer and whatever notes you want to use. Exam in room 112+118 in building 210.

Re-exam.

In case there is a need for a re-exam it will be ? 2013 (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:

kursus databasen


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.


Reporting

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.

Campusnet aflevering

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:

 s12345.doc
 s12345.1.doc
 s12345.2.doc
 s12345.homology.txt


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

DNA translation table

Amino acids

  • Databases

UniProt database

PDB protein DataBank

Genbank

  • Substitition matrices

Substitution matrices introduction

Blosum62 matrix

  • Alignment tools

Pairwise sequence alignment Embl-ebi

Blast via ncbi

Exam from previous years


Lecture Plan 2012 - 2013

Please note: lecturers may be working on slides and other course material until the last minute, so changes may occur!

Thursday November 15

Lecture 1 - Introduction to the course - Thomas Nordahl Petersen
Slides
Lecture 2 - Biological information, DNA structure and sequencing, GenBank searching - Henrik Nielsen.
Readings:
Slides:
Handouts:
Lecture 3 - DNA, Amino Acids and Proteins - Thomas Nordahl Petersen.
Readings:
Slides:


Exercises - Henrik Nielsen. (Exercise helper: Bent Petersen.)
  1. Exercise: Searching the GenBank database NB: I behøver ikke at svare på spørgsmål 1.3 eller på spørgsmål 3!
  2. Exercise: The protein database UniProt

Thursday November 22

Lecture 1 - Evolution and DNA - Anders Gorm Pedersen
Reading:
Slides:


Lecture 2 - Amino acids & proteins part II - Thomas Nordahl Petersen
Readings
Slides:
Exercises: Thomas Nordahl Petersen
Learning amino acid properties by use of modeling kit - modeling by hand



Thursday November 29

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


Exercises




Thursday December 6

Lecture 1 - Introduction to Blast - Thomas Nordahl Petersen
Readings:
Slides:
Handouts:


Lecture 2 - Psi-Blast - Iterative Blast searches and Position Specific Scoring Matrices - Bent Petersen
Readings:
Slides:
Exercises: Thomas Nordahl Petersen - Bent Petersen
  1. Using Blast for sequence searches

Thursday December 13

Lecture 1 - Multiple alignments - Anders Gorm
Slides
Readings:
Exercise 1
Extra material:
  • Fun multiple alignment "game": Phylo


Lecture 2 - Pylogenetic trees - Anders Gorm
Slides:
Readings
Handouts:
Exercise 2

Thursday December 20

Lecture 1 - Protein 3D-structure - Thomas Blicher
Readings
Lecture 2 Homology modeling - Thomas Blicher
Readings:


Slides:
Exercises: Thomas Blicher - helper: Henrik Marcus Geertz-Hansen

Thursday January 3

Lecture 1 - Introduction to neural networks - Thomas Nordahl Petersen
Slides:


Exercise 1: Thomas Nordahl Petersen
Exercise 2: Thomas Nordahl Petersen

Thursday January 10

Lecture 1 - Genome Browsers - Thomas Nordahl Petersen
Slides:
Readings:
Exercises:


Lecture 2 - From genotype to phenotype - Valborg Gudmundsdottir
Slides:
Exercises:

Thursday January 17

Lecture 1 - Entropy, Information Content & logo plots - Thomas Nordahl Petersen
Readings:
Handouts:
Slides:


Lecture 2 - Summary - Thomas Nordahl Petersen
Slides:
Exercises: Thomas Nordahl Petersen
  • Logo Plots pdf
  • Logo Plots doc

Monday January 21 exam

Exam
  • 4 hour written exam from 9-13 room 112+118, building 210
  • 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 examJan2013 docx once exam has started
  • Link to examJan2013 pdf once exam has started

Monday 25 February 2013 - re-exam (mundtlig)

 Såfremt du/I ikke har bestået den skriftlige eksamen, er der mulighed for at gå op til
 en mundtlig eksamen. Man tilmelder sig ved at sende en mail til mig tnp@cbs.dtu.dk med navn og studienummer senest d 18 Feb.
 Du skal møde op i bygning 208, rum 062 i kælderen (indtil middag, 027 efter middag) og trække et spørgsmål,
 herefter får du forberedelse som foregår i rum 012 A (byg 208), hvor censor eller jeg lige følger dig på plads.
 Kom forberedt og medbring de bøger/noter som du vil samt en computer.


 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. Rækkefølgen og tidspunkt vil
 blive vist herunder. 
Nummer 1-6 skal trække spørgsmål i rum 062 (kælderen), bygning 208
Nummer 7-10 skal trække spørgsmål i biblioteket rum 027 (stue-etagen), bygning 208
Forberedelsen foregår i rum 012A (stue-etagen), Bygning 208
1  Thomas Sørensen (s114637)      - Trække spg kl 8:30  (eksamen kl  9:05-9:25)
2  Reem Intissar Hassan (s114168) - Trække spg kl 9:05  (eksamen kl  9:40-10:00)
3  Anastasia Kristensen (s114181) - Trække spg kl 9:40  (eksamen kl 10:15-10:35)
4  Lise Marie Petersen (s080480)  - Trække spg kl 10:15 (eksamen kl 10:50-11:10)
5  Arif Mustafa (s072825)         - Trække spg kl 10:50 (eksamen kl 11:25-11:45)
6  Rishigeshan Balachandran (s104128) - Trække spg kl 11:25 (eksamen kl 11:50-12:10)
pause
7  Hiba Marwan (s104115)          - Trække spg kl 13:00 (eksamen kl 13:35-13:55)
8  Razia Haqani (s104127)         - Trække spg kl 13:35 (eksamen kl 14:10-14:30)
9  Carsten Lønberg (s114144)      - Trække spg kl 14:10 (eksamen kl 14:45-15:05)
10 Summia Nadeem (104130)         - Trække spg kl 14:45 (eksamen kl 15:20-15:40)


Når I har trukket et spørgsmål til eksamen vil I få udleveret det i papirform, men der vil også være en elektronisk version som I kan klikke på herunder med navn Spg1 - Spg9. Den elektronoske version vil først blive aktiveret efter I har trukket jeres spørgsmål og deaktiveret igen efter eksamen.

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