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27619 Perl and Unix for Bioinformaticians

Danish title:

Perl og Unix for bioinformatikere

Language:

Point( ECTS )

10

Course type:

MSc
Taught under open university
Generel competence course, MSc. Eng., Bioinformatics Systems Biology

Schedule:

F2A (mon 13-17) and F2B (thurs 8-12)

Location:

Campus Lyngby

Scope and form:

Lectures and computer exercises

Duration of Course:

13 weeks

Date of examination:

F2A, E2A

Type of assessment:

Exam duration:

Aid:

Evaluation:

Previous Course:

27013 and 27613

Not applicable together with:

Participants restrictions:

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.

Learning objectives:

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 project.
  • 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 behavior.
  • Evaluate the running time of programs.
  • Parse (read and extract) (bioinformatic data) files for needed information.
  • Define and use regular expressions (computational pattern recognition).
  • Write code so others can understand it, and understand others code.

Content:

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.

Remarks:

Students will regularly evaluate each others code.

Responsible:

Peter Wad Sackett , Building 208, room 020, Ph. (+45) 4525 2427 , pws@cbs.dtu.dk

Department:

27 Department of Systems Biology

Home page:

http://www.cbs.dtu.dk/courses/27619/

Registration Sign up:

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Last updated: 05. maj, 2014