Difference between revisions of "MBV-INFX410 2016"

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(Bioinformatics for Molecular Biology - 2016)
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=== Required reading material / Curriculum ===
 
=== Required reading material / Curriculum ===
 
The curriculum comprises all lectures, lecture handouts and exercises. In addition to the articles listed below:
 
The curriculum comprises all lectures, lecture handouts and exercises. In addition to the articles listed below:
 +
 +
The following articles/reviews/written material '''''is part of the curriculum''''' for MBV-INF4410 and MBV-INF9410:
 +
 +
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]
 +
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]
 +
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130  Nucleic Acids Res. <b>43</b>, D6 (2015)]
 +
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]
 +
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]
 +
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]
 +
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]
 +
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]
 +
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]
 +
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]
 +
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]
 +
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]
 +
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]
 +
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]
 +
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]
 +
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]
 +
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]
 +
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]
 +
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]
 +
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]
 +
 +
=== Other good articles (''not ''curriculum) ===
 +
 +
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]

Revision as of 12:40, 4 October 2016

Bioinformatics for Molecular Biology - 2016

UNDER CONSTRUCTION!!!!!

All students must be present at the start of the course, at 09:15, on November 14. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See contact details below).

This is the wiki for the courses MBV-INF4410 and MBV-INF9410 offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.

The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.

Here is an overview of the course. The contents of the different lectures and exercises will be available shortly.

Week 46 Week 47 Week 48 Week 49 Week 50
Mon Lectures/

exercises

Lectures/

exercises

Obligatory

home assignment

Lectures/

exercises

Exam start

(home assignment)

Tue Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Wed Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Thu Lectures/

exercises

Lectures/

exercises

Home assignment Lectures/

exercises

Exam start

(home assignment)

Fri Lectures/

exercises

Lectures/

exercises

Hand in

home assignment

Lectures/

exercises

Exam end

(home assignment)

Time and place

Room 1250, 1st floor of Biology Buiding (Kristine Bonnevies Hus).

Detailed program

The program is still under development and may be updated. The times listed here are only tentative and may likely change. We will mix in small breaks and try to have a lunch break between 13:00 - 14:00.

Week Monday Tuesday Wednesday Thursday Friday
46 Nov 14 Nov 15 Nov 16 Nov 17 Nov 18
09:15 - 11:00:

Course introduction (lecture)

11:15 - 13:00:

Biological databases,

Unix (lectures/exercises)

14:15 - 16:00:

Basic Unix (excercises)

09:15 - 11:00:

Ensembl genome browser

and Jalview (lectures/demo)

11:15 - 13:00:

Working with sequences

and databases (lectures/exercises)

14:15 - 16:00:

Applied sequence bioinformatics

09:15 - 11:00:

More Unix and

UCSC genome browser (lectures/exercises)

11:15 - 13:00:

Galaxy / Life Portal (lectures/exercises)

14:15 - 16:00:

09:15 - 16:00:

Python workshop

(lectures / exercises)

09:15 - 16:00:

Python workshop

(lectures / exercises)

47 Nov 21 Nov 22 Nov 23 Nov 24 Nov 25
09:15 - 16:00:

Sequence searching and alignments

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

09:15 - 16:00:

Structural bioinformatics

(lectures and exercises)

Docking and drug discovery

Practical Unix/Python exercise

Reproducibility /

Statistical epigenomics

48 Nov 28 Nov 29 Nov 30 Dec 1 Dec 2
Obligatory home assignment Obligatory home assignment Obligatory home assignment Obligatory home assignment Hand in home assignment
49 Dec 5 Dec 6 Dec 7 Dec 8 Dec 9
Introduction to statistical inference and R

Basic R and exploring your data

Analysis of gene expression using R NGS Last course day

What does it men to do bioinformatics?

Gene lists and over-representation analysis

Summary

Hand out exam
50 Dec 12 Dec 13 Dec 14 Dec 15 Dec 16
Home exam Home exam Home exam Home exam Hand in exam

Contacts

Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582

Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no

Required reading material / Curriculum

The curriculum comprises all lectures, lecture handouts and exercises. In addition to the articles listed below:

The following articles/reviews/written material is part of the curriculum for MBV-INF4410 and MBV-INF9410:

Other good articles (not curriculum)