210007 BioLinux: Bioinformatics and Linux Course

Details
Department of Bacic Animal and Veterinary Sciences
Department of Basic Science and Environment   0 %
Earliest Possible YearBSc. 2 year to Post experience Master´s Programme
DurationOutside schedule
 
Credits7.5 (ECTS)
Course LevelJoint BSc and MSc
Can also be taken as a Ph.D. course
 
ExaminationFinal Examination

written examination


All aids allowed

Description of Examination: Evaluation of a report based on the students own data or data handed out by the teachers. A report is turned in by the end of the course.

Weight: report 100%



7-point scale, internal examiner
 
Organisation of TeachingLectures, computer exercises and project work
 
Block PlacementSummer Course
Week Structure: Outside schedule, Lecures will take place 10-21 August (on 12 and 19 August there will be no lectures). Deadline for submission of report: 23 September.
 
Teaching LanguageEnglish
 
Optional PrerequisitesBasic knowledge to genetics, computers, mathematics and statistics
 
RestrictionsNone
 
Course Contents
The main topics in the course:
Introduction to basic concepts in bioinformatics, within the context practical processing large amounts of data. 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://genome.ku.dk/courses/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://genome.ku.dk/courses/biolinux
 
Learning Outcome
Knowledge and understanding:
To identify the relevant parts of processing data where automation is needed. To know that webservers in general are way insufficient to carry out bioinformatical analyses and that they prevent the user from doing relevant types analyses. That is to know that "Clicking does not scale". To implement perl and shell scripts to process the data. To write up and present an overview of the pipeline for data processing. In the process to show an overview of the basic data relevant processing concepts from bioinformatics.


Skills:
To process and analyze biological sequence (and related) data and apply concepts from bioinformatics within the process. To apply concepts from perl and shell to implement the data processing scripts. To integrate and process data from multiple sources. To analyze data within a commandline context. To be able to work close with non-speciliast scientists, such as lab-people within a team and thereby be able to implement on demand solutions for problems appearing.

Competences:
To work independently and apply concepts of perl and shell scripting to develop processing pipelines of biological sequence (and related) data. To critically assess and evaluate the result of the dataprocessing.

 
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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