| Department of Bacic Animal and Veterinary Sciences
50 % Department of Natural Sciences 50 % | |||
| Earliest Possible Year | 5 to 7 | ||
| Duration | 1 semester | ||
| Credits | 6 (ECTS) | ||
| Course Level | Joint BSc and MSc | ||
| Examination | evaluation of project report Aid allowed Description of Examination: 13-point scale, internal examiner | ||
| Organisation of Teaching | |||
| Block Placement | outside schedule Forelæsninger onsdag kl. 11.10-12.30, øvelser onsdag 13.15-16:00 | ||
| Teaching Language | English | ||
| Optional Prerequisites | 015311 Mathematics, basic course 010611 Statistics, Basic Course 045121 046111 103118 | ||
| 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. (see http://bioinf.kvl.dk/biolinux) | |||
| 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." (see 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. (see 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. (http://www.oreilly.com/catalog/bioskills/) * Learning Perl, 3rd Edition. Randal L. Schwartz and Tom Phoenix.O'Reilly & Associates Inc. Sebastopol, CA, USA. (http://www.oreilly.com/catalog/lperl3/) Supplementary: * Beginning Perl for Bioinformatics. James Tisdall.O'Reilly & Associates Inc. Sebastopol, CA, USA. (http://www.oreilly.com/catalog/begperlbio/) | |||
| 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 | |||
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