210007 BioLinux: Bioinformatics and Linux Course

Details
Department of Bacic Animal and Veterinary Sciences   60 %
Department of Natural Sciences   40 %
Earliest Possible YearBSc. 2 year
DurationOne block
 
Credits7.5 (ECTS)
Course LevelJoint BSc and MSc
Common for bachelor, "Kandidat", ph.d. and "uddannelseskursus" as it gives a separate, specific and uniq competences.
 
ExaminationFinal Examination

written examination


All aids allowed

Description of Examination: Evaluation of report based on the students own data or data handed out by the teachers.

Weight: report 100%



13-point scale, internal examiner
 
Organisation of TeachingLectures,computer exercises and project work
 
Block PlacementBlock 2
Week Structure: C
 
Teaching LanguageEnglish
 
Optional PrerequisitesBasic knowledge to genetics, computers, mathematics and statistics.
 
Areas of Competence the Course Will Address
Scientific:
The aim of the course is to introduce basic concepts of bioinformatics, along with basic concepts of Linux and the Perl script language such that the student is able to construct the needed tools for automated analysis of biological sequences. The student should also aquire basic skills to navigate in a bioinformatics command line environment.

Technology and prodcution
To apply the aquired knowledge as a part of a larger set up.

Ethics and values:
To critically communicate research results.


Details can be found at http://bioinf.kvl.dk/biolinux
 
Course Objectives
The aim of the course is to introduce basic concepts of bioinformatics, along with basic concepts of Linux and the Perl script language such that the student is able to construct the needed tools for automated analysis of biological sequences. The student should also aquire basic skills to navigate in a bioinformatics command line environment.
Details can be found at the course homepage.
 
Course Contents
The main topics in the course:
Introduction to basic concepts in bioinformatics. Introdcution to linux (the command line etc.). Perl and shell scripts.
Conversion between dataformats (incl. processing of blast output).
Implementing alignment algorithms.
Applying bioinformatics algorithms.
Integrating bioinformatics software.

Motivation
Today, even fairly small labs can generate a substantial amount of biological sequence data. However, to make use of these data in further experimental analysis as well as gaining insight in biological problems, efficient and task specific computational tools are required. Even though some of these tools are available online, they are often limited in resources and requires much manual intervention. This is true even of many otherwise user-friendly commercial bioinformatics packages: they automate some analysis tasks well, but make the automation of other tasks substantially more complicated and demanding than necessary. The bioinformatic challenges in designing methods and specific tools can be well coped with in the Linux (Unix) operating system. In addition, specific tools and existing programs, can well be implemented and integrated by the scripting language Perl. Motivation, however, is more than just applying tools, but also to use and develop them to gain insight in molecular mechanisms.

Finally, it can be a time saving factor, as expressed by Alan Bleasby (The Biochemist, Oct. 1997): Two months in the lab can easily save an afternoon on the computer.

Details can be found at http://bioinf.kvl.dk/biolinux
 
Teaching And Learning Methods
Even though the lectures mainly will provide an overview of relevant topics (and go in detail with the hard ones), students will be expected to take actively part of the problems discussed in the lectures. Not all reading material will be addressed during the lectures, but will still be a necessity for the exercises. In the exercises the students will be faced with a number of practical bioinformatic problems they should solve. If the exercises are not completed within the available time, they are to be considered as home work and should be completed before next week exercises. Note that exercises might be based on previous solved exercises. Details can be found at http://bioinf.kvl.dk/biolinux
 
Course Litterature
Course will be based on the following books, but other material might also be handed out:

Developing Bioinformatics Computer Skills.
Cynthis Gibas and Per Jambeck.O'Reilly & Associates Inc. Sebastopol, CA, USA.(We refer to this book in the schedule as the bioinf-book.)Order it on amazon.
Learning Perl, 3rd Edition. Randal L. Schwartz and Tom Phoenix.O'Reilly & Associates Inc. Sebastopol, CA, USA.(We refer to this book on the schedule as the perl-book.)Order it on amazon.

Supplementary material:
Beginning Perl for Bioinformatics. James Tisdall.O'Reilly & Associates Inc. Sebastopol, CA, USA.

 
Course Coordinator
Jan Gorodkin, gorodkin@genome.ku.dk, Department of Basic Animal and Veternary Sciences/Genetics & Bioinformatics, Phone: 35333578
 
Study Board
Study Committee NSN
 
Course Scope
lectures30
practicals40
project work81
supervision5
preparation50

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