210007 BioLinux: Bioinformatics and Linux Course

Detaljer
Inst. for Basal Husdyr- og Veterinærvidenskab
Inst. for Grundvidenskab og Miljø   0 %
English titleBioLinux: Bioinformatics and Linux Course
Tidligst mulig placeringBachelor 2. år til Master udd. (efteruddannelse)
VarighedUdenfor blokstruktur
 
Pointværdi7.5 (ECTS)
KursustypeFælleskursus
Can also be taken as a Ph.D. course
 
EksamenSluteksamen

skriftlig prøve


Alle hjælpemidler tilladt

Beskrivelse af eksamen: 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.

Vægtning: report 100%



7-trinsskala, intern censur
 
Rammer for undervisningLectures, computer exercises and project work
 
BlokplaceringSummer Course
Ugestruktur: 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.
 
UndervisningssprogEngelsk
 
Anbefalede forudsætningerBasic knowledge to genetics, computers, mathematics and statistics
 
Begrænset deltagerantalNone
 
Kursusindhold
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
 
Undervisningsform
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
 
Målbeskrivelse
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.

 
Litteraturhenvisninger
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.

 
Kursusansvarlig
Jan Gorodkin, gorodkin@genome.ku.dk, Institut for Basal Husdyr- og Veterinærvidenskab/Genetik & Bioinformatik, Tlf: 35333578
 
Studienævn
Studienævn NSN
 
Kursusbeskrivelsesomfang
forelæsninger30
praktiske øvelser40
projektarbejde81
vejledning5
forberedelse50

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