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About course

DD2404 Applied Bioinformatics 7.5 credits

Administer About course

Bioinformatics has become an important tool for handling and utilizing the large sets of valuable data produced in Molecular Biology. Computerized analysis has a role both as support for wet-lab projects and as a means of extracting knowledge from already available datasets. The fast-growing amount of data makes it necessary to be able to automate analysis and make analysis on a very large scale. This course aims to introduce techniques for meeting this challenge.

Course offerings are missing for current or upcoming semesters.
Headings with content from the Course syllabus DD2404 (Autumn 2012–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

Working in Unix. A quick introduction to Python. Good practice for scientific programming. Important modules for scientific programming.

Terminology and methods in Bioinformatics. Sources of data in Bioinformatics. Databases and basic SQL. 

Some of the course contents is useful in many contexts, but we will focus on applications in Bioinformatics.

Intended learning outcomes

After completion of this course, you will be able to

  • structure data for efficient computerized storage and analysis
  • use relational databases
  • create your own relational databases
  • use a scripting language to solve every-day problems in Bioinformatics
  • use important Bioinformatic software libraries to quickly find solutions for tedious programming problems.

Literature and preparations

Specific prerequisites

Single course students: 90 university credits including 45 university credits in Mathematics or Information Technology. English B, or equivalent.

Recommended prerequisites

For those already studying at KTH: introductory computer programming, for example DD1310, DD1321 or DD1322.

Equipment

No information inserted

Literature

The course literature will be announced at the home page for the course at least 4 weeks before course start.

Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

A, B, C, D, E, FX, F

Examination

  • LAB1 - Laboratory Assignments, 4.5 credits, grading scale: A, B, C, D, E, FX, F
  • PRO1 - Project, 3.0 credits, grading scale: P, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

In this course all the regulations of the code of honor at the School of Computer science and Communication apply, see: http://www.kth.se/csc/student/hederskodex/1.17237?l=en_UK.

Opportunity to complete the requirements via supplementary examination

No information inserted

Opportunity to raise an approved grade via renewed examination

No information inserted

Examiner

Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study

Biotechnology, Computer Science and Engineering, Information Technology, Information and Communication Technology

Education cycle

Second cycle

Add-on studies

DD2399 Omic Data and Systems Biology

Contact

Lars Arvestad, e-post: arve@kth.se

Supplementary information

This course replaces the course DD2397 with the same name from autumn term 2012.