View source for Fundamentals of Bioinformatics 2011-2012

{{Header Bioinformatics}}
==Schedule==
[[Media:FoB Schedule 2011.pdf | Course Manual and Schedule.pdf]]
* Rooms for the lectures have been updated. You can also [http://vurooster.nl/course/X_405052 check the schedule at vurooster.nl]
* Times for the programming class and the project have been updated, as communicated earlier.
* The planning of the programming classes has changed, we now continue into week seven (Mon 17/10 and Tue 18/10) because of that - please adjust your agenda's accordingly.
* The ordering and days of the last three lectures has changed. We now have one lecture in week 6, on Mon 10/10.
* Last assignment in programming class is canceled, and updated Project schedule. 


===Presentations===
* Friday, October 28, 9.00-16.30 there will be the mini symposium 'Bioinformatics meets Systems Biology' where all students from the Fundamentals of Bioinformatics and the Introduction to Systems Biology courses will present their work.
** [[Media:Minisymposium Bioinformatics meets Systems Biology.pdf|Programme 'Bioinformatics meets Systems Biology']]
* We will be in [[Media:Artis-plattegrond-42.pdf|Artis - Building 42]] (highlighted in a yellow circle).
** Artis will open at 9.00, and it will take you another 10-15 minutes to get to the right building. With the busy schedule, please be in time! 


===Question Hour===
* Monday October 24, 9.00-11.00 we will have a question hour for the exam (location to be announced - please come to P1.36 if you do not hear otherwise)


===Exam===
* The exam will be on Thursday October 27 from <font color=red>'''8.45-12.00'''</font><strike>10.00-13.00</strike> (C147)
* [[FoB 2010 Exam Questions|Example Questions]]
* [[Media:FoB Learning Objectives.pdf|Learning Objectives]]


===Additional Lectures===
* Prof Alan Mark (Queensland University, Brisbane, Australia):<br> "''Atomistic models of biomolecular systems: the search for certainty in an uncertain world''"
** Time: Tuesday 13th of September, 13.00 h
** Location:  M-639
** if you are interested in '''protein modeling''', you simply cannot miss this!


==Classes==

N.b.: these classes are a part of the courses ''Fundamentals of Bioinformatics'' and ''Introduction to Systems Biology''. You '''do not''' need to register for these classes (also not at the UvA).

===Programming classes===
[[Bioinformatics Programming Classes 2011-2012 | Programming Classes]]

===Biology classes===
* organized and given by Prof Joost Teixeira De Mattos
{|class="wikitable" cellspacing="6"
|-
! Day	!! Time 	!! Room 	!! Lecturer
|-
| Friday Sept 9 	|| 9.15-13.00	|| F1.24C	|| Klaas Hellingwerf
|-
| Friday Sept 16	|| 9.15-13.00	|| F3.21	|| Joost Teixeira De Mattos
|-
| Friday Sept 23	|| 9.15-13.00	|| F3.21	|| Joost Teixeira De Mattos
|-
| Friday Sept 30	|| 9.15-13.00	|| F3.21	|| Joost Teixeira De Mattos
|-
| Friday Oct 7  	|| 9.00-13.00	|| F2.19 	|| Klaas Hellingwerf
|-
| Friday Oct 14 	|| 9.00-13.00	|| F2.19	|| Klaas Hellingwerf
|}
* '''Test/exam:''' 
** date: '''Friday October 21''' 
** time: '''10.00'''
** place: '''F3.21''' in the NIKHEF building (see below)

(all in [[Media:A5_plattegrond_SPA_Engels_web.pdf | Nikhef building, Science Park 105]], ask one of our UvA students!)

* Recommended book: ''Molecular Biology of the Cell'' by Alberts et al.; Garland Science, 2008.

* If, after approval by one of us (Jaap, Bas, Sanne, Douwe or Anton), you do this in self-study, you may consider signing up for the [http://www.ncsb.nl/e-courses NCSB course ''Module I: Basic biology for non-biologists'']. The site mentions a fee of &euro;50, which you should not need to pay -- please contact us if you hear otherwise.

.

===Mathemathics classes===
[[Mathematics]]



==Project==
[[Practical Project 2011-2012]]

==Reading materials==
The course book is: Marketa Zvelebil and Jeremy O. Baum Understanding Bioinformatics, Garland Science 2008 ISBN-10: 0-8153-4024-9

Recommended reading: Larry Hunter's "Molecular biology for computer scientists". This is a nice and concise description of the most important concepts in molecular biology, explained with the non-biologist in mind. It is a useful document for revising your knowledge.
*[[Media:Hunter.pdf | Hunter.pdf]]

Jin Xiong's ''Essential Bioinformatics'' is a nice read providing a good overview of a number of important aspects of bioinformatics. Written to serve as bedside reading! Parts of this book are to be found 
[http://bb.vu.nl/bbcswebdav/courses/FEW_X_405052_2011_110/Essential-Bioinformatics-Xiong.pdf here].


===Paper discussion===
Papers to read for Monday October 17, 11.00-12.00 in P3.37:

* [[Media:PNAS-1998-Brenner-6073-8.pdf | Brenner, Chothia & Humbard]]
* [[Media:SCIENCE-2007-Rapp.pdf | Rapp, Sepp&auml;l&auml;, Granseth & von Heine]]

The papers are on homology detection and benchmarking - you'll recognize that topic. Within each Project Group, please assign two (or three) people to each paper. So each of you only needs to read and prepare for discussion for one paper.

For further reading on this topic, please refer to:

* Reid AJ, Yeats C, Orengo CA. Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. Bioinformatics. 2007 23:2353-60.
* Rapp M, Granseth E, Seppälä S, von Heijne G. Identification and evolution of dual-topology membrane proteins. Nat Struct Mol Biol. 2006 13:112-6.

.

==Lectures==
{|
|-
!Lecture Topic   !! Slides   !! Handouts   !! Reading
|-
|Lecture 1| General
|[[Media:FoB_lec1.pdf | FoB_lec1.pdf]]
|[[Media:FoB_lec1_handout.pdf | FoB_lec1_handout.pdf]]
|-
|Lecture 2| Genomics 1
|[[Media:FoB_lec2.pdf | FoB_lec2.pdf]]
|[[Media:FoB_lec2_handout.pdf | FoB_lec2_handout.pdf]]
|-
|Lecture 3| Genomics 2
|[[Media:FoB_lec3.pdf | FoB_lec3.pdf]]
|[[Media:FoB_lec3_handout.pdf | FoB_lec3_handout.pdf]]
|-
|Lecture 4| Ontologies and GO
|[[Media:FoB_lec4.pdf | FoB_lec4.pdf]]
|
|-
|Lecture 5| Protein Bioinformatics 1
|[[Media:FoB_lec5.pdf | FoB_lec5.pdf]]
|[[Media:FoB_lec5_handout.pdf | FoB_lec5_handout.pdf]]
|Chapter 12 Essential Bioinformatics OR Chapter 2 Understanding Bioinformatics
|-
|Lecture 6| Protein Bioinformatics 2.
|[[Media:FoB_lec6.pdf | FoB_lec6.pdf]]
|
| [http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2119.html Viral protein structure solved by FoldIt game and X-ray crystallography Nature 2011, September 18]
|-
|Lecture 7| Petri-net modeling
|[[Media:FoB_lec7.pdf | FoB_lec7.pdf]]
|
|-
|Lecture 8| Secondary Structure prediction
|[[Media:FoB_lec8.pdf | FoB_lec8.pdf]]
|
|-
|Lecture 9| Repeat and Domain prediction.
|[[Media:FoB_lec9.pdf | FoB_lec9.pdf]]
|[[Media:FoB_lec9_handout.pdf | FoB_lec9_handout.pdf]]
|-
|Lecture 10| Next Generation Sequencing
|[[Media:FoB_lec10.pdf | FoB_lec10.pdf]]
|[[Media:FoB_lec10_handout.pdf | FoB_lec10_handout.pdf]]
|[http://www.nature.com/nmeth/journal/v6/n11s/full/nmeth.1376.html Flicek  & Birney], see Blackboard
|-
|}

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