BioinfHumanBio2011

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Bioinformatics for Human Biologists - January 2011

In 2011 the course runs from monday the 3rd till friday the 7th of january.

Course homepage: Bioinformatics for Human Biologists

General Information

Where and When

January 3rd - 7th, 2011 - Technical University of Denmark (Lyngby Campus): Room 162 / Building 210. Directions on how to get to DTU (Lyngby) and a map of the buildings are found here: DTU Directions.

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

The course is pass/fail based on participation (both lectures and exercises).

Hardware / Software used

First and foremost: YOU MUST BRING YOUR OWN LAPTOP TO THE COURSE - wireless access will be provided. For the PyMOL exercise Wednesday, please bring a 3-button / scrollwheel mouse as well.

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: http://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: http://www.jedit.org.

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

Free Student's version:

Reporting

Each group has to keep a "log book" with answers to the questions asked in the exercises. After completing an exercise, mail in the report: raz+humanbio@cbs.dtu.dk

The log book should be kept as minimalistic as possible - the important thing here is to simply focus on giving a nice and simple overview of you answers and not to spent 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:

  1. Assessing participation in the exercises.
  2. As a means to improve our teaching, since we get a chance to learn what questions are typically difficult to answer or understand.

Exercise hand-ins

Table of exercise reports that has been mailed in:

(Will be updated each day)

Lecture plan

Monday (Jan 3rd)

9.15 - 12.00
Lecture: Introduction to the course. DNA and evolution - DNA databases (Rasmus Wernersson)
Readings:
Handouts:
Exercise: Searching the GenBank database
13.00 - 16.30
Lecture: Proteins and Protein databases (Rasmus Wernersson/Henrik Nielsen)
Readnings:
Exercises: 1) Virtual translation of DNA sequences, 2) Exploring the UniProt database

Tuesday (Jan 4th)

9.15 - 12.00
Lecture: Pairwise alignment (Anders Gorm Pedersen / Rasmus Wernersson)
Readings: Page 35-55 in Immunological Bioinformatics
Exercise: Pairwise alignment using EBI resources
13.00 - 16.00
Lecture: BLAST - sequence based database searching (Anders Gorm Pedersen / Rasmus Wernersson)
Handouts:
Exercise: Using BLAST - statistics & results

Wednesday (Jan 5th)

9.15 - 12.00/12.30
Lecture: Multiple alignments (Anders Gorm Pedersen / Rasmus Wernersson)
Lecture: Pylogenetic trees (Anders Gorm Pedersen / Rasmus Wernersson)
Readings:
Software: Download FigTree from here: http://tree.bio.ed.ac.uk/software/figtree/
Exercises: 1) Multiple alignment, 2) Phylogenetic trees
13.00 - 16.30
Lecture: Protein structure and the PDB database (Thomas Holberg Blicher)
Exercise: Using PyMol for visualizing and analyzing protein 3D structure

Thursday (Jan 6th)

9.15 - 12.00
Lecture: Human Genome Browser (Thomas Nordahl Petersen)
Slides: GenomeBrowser.ppt
Exercise: Genome Browser exercise (PDF)
13.00 - 16.30
Suggested readings:
Lecture: Next generation sequencing and assembly (Kasper Nielsen)
Slides: Second generation sequencing (PDF)
Mini-exercise: De-novo assembly
Mini-exercise: Mapping reads to reference genome
Lecture: SNPs and genome-wide association studies (Kasper Nielsen)
Slides: Genome Wide Association Studies (PDF)
Mini-exercise: Comparing GWAS results (NHGRI GWAS catalog)
Lecture: Reconstructing the past: The First Ancient Human Genome (Kasper Nielsen)
Slides: Ancient genome (PDF)
Exercise: From Genotype to Phenotype

Friday (Jan 7th)

9.15 - 12.00
Lecture: Prediction methods in immunological bioinformatics (Claus Lundegaard/Morten Nielsen/Ole Lund)
Readings: page 91 to 102 in Immunological Bioinformatics
Exercise: Prediction methods
13.00 - 16.30
Lecture: PSI-BLAST (Morten Nielsen/Ole Lund/Claus Lundegaard)
Readings: page 68 to 80 in Immunological Bioinformatics
Exercise: Psi-BLAST - hunting for proteins in the twilight-zone
PHYRE EXAMPLE: http://www.sbg.bio.ic.ac.uk/phyre/qphyre_output/38a23a5b367c6340/summary.html

Future projects: contact information

We very much welcome Master Thesis projects from students at the Human Biologist study line (PhD project as well). Such projects are typically coordinated with the individual research group at the Center - a full list is here:

Obvious choices for collaboration would for example be the Immunological Bioinformatics, Functional Human Variation and Integrative Systems Biology groups.

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