27619 Perl and Unix for Bioinformaticians
|Perl og Unix for bioinformatikere|
Point( ECTS )
Taught under open university
|Generel competence course, MSc. Eng., Bioinformatics Systems Biology|
|F2A (Mon 13-17) and F2B (Thurs 8-12)
Scope and form:
|Lectures and computer exercises|
Duration of Course:
Type of assessment:
|27013 and 27613|
Not applicable together with:
|Minimum 12 Maximum: 40|
General course objectives:
The student should be able to solve minor bioinformatic problems in
a structured manner using Perl in a Unix environment, for example
during project work.
A student who has met the objectives of the course will be able to:
- Use various data types and built-in functions in Perl.
- Demonstrate insight in structured problem solving.
- Recognize patterns in data and generalize from them.
- Analyze and plan the execution of a minor computational
- Design and implement an efficient algorithm in Perl.
- Decompose a computational task using sub-routines.
- Find and correct errors in a program based on its
- Evaluate the running time of programs.
- Parse (read and extract) (bioinformatic data) files for needed
- Define and use regular expressions (computational pattern
- Write code so others can understand it, and understand others
This course provides an introduction to elementary Unix and the
Perl programming language following basic programming principles
and good programming practices. The Unix introduction covers basic
commands, file manipulation and input/output redirection. In Perl,
various looping and control structures, built-in data and container
types (arrays and hashes), regular expressions and more advanced
data structures are covered. As an example, common bioinformatic
file formats are parsed and manipulated. A large part of the course
is spent on computer exercises which are integrated with the
lectures. Students will get a minor programming project during the
course, possibly a project of their own design.
Students will regularly evaluate each others code.
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Last updated: 22. august, 2014