Bioinformatics

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Welcome to BB2441 Bioinformatics (7.5 credits)

Please note that this page is for general information only. We will use Canvas (https://kth.instructure.com/) for all further information and communication regarding this course.

Important dates for BB2441 fall 2017:

  • 2017-08-28 Course starts in FB54 AlbaNova University Center
  • 2017-09-05 Last day to sign up for Quiz
  • 2017-09-20 or 09-21 (TBD) Quiz (Kontrollskrivning)
  • 2017-10-05 Last day to sign up for Exam
  • 2017-10-25 Exam 08:00-12:00
  • 2017-12-21 Re-exam 14:00-19:00

Intended learning outcomes

The aim of the course is that the students should acquire sufficient knowledge about fundamental bioinformatics and programming resources and methods, so as to know how to (i) explain the theory behind the methods, (ii) use the corresponding tools and resources to perform analyses of molecular biology data, and (iii) interpret the results of these analyses.

 Specifially, after passing the course, the student should be able to:

  1. explain the significance of bioinformatics in modern life science
  2. explain the applications and limitations of bioinformatical methods
  3. explain fundamental bioinformatical methods
  4. use relevant bioinformatical tools to solve bioinformatical problems
  5. motivate the choice of bioinformatical tools
  6. interpret the results of bioinformatical analyses
  7. use script programming to perform fundamental bioinformatical operations
  8. use fundamental commands in Unix/Linux or equivalent

Course contents

Bioinformatics: Pairwise sequence alignment of protein and DNA/RNA sequences, multiple sequence alignment, significance of alignment results, features of protein and DNA/RNA sequences including sequence conservation, homology, phylogeny, gene expression and differential gene expression, clustring of vectors, introduction to relevant public databases and extraction of relevant data from these. How to use command line operations for data analysis and file management (in Unix/Linux, or corresponding operating systems), as well as available web based tools for data analysis (e.g., Galaxy).

Programming: reading from file, basic operations on data such as conditional execution, loops, and regular expression, as well as writing to file.

In total 20 lectures and 7 computer exercises.

Literature

Text book for the bioinformatics part: Exploring bioinformatics. A project-based approach. Caroline St. Clair and Jonathan E. Visick (Jones & Bartlett Learning, 2nd edition) ISBN 978-1-284-03424-0.

Text book for the programming part: TBD

Additional reading (e.g., relevant scientific articles) will be specified during the course. The course contents is the union of all material presented at the lectures, at the computer exercises, and in the course literature as specified by the detailed reading assignments, as well as any additional handouts or other resources specified during the course.

Canvas will be used for course information and communication

Canvas will be used for communication during the course, including any updates to this course information. Your access to the BB2441 event in Canvas will be activated after you have registered at the course. Then you may log in at https://kth.instructure.com/ using your kth.se-account and look for the event BB2441 Bioinformatics. Lecture notes, lab instructions, and other handouts will be provided through Canvas.

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All courses at KTH are not using the course web in full. The course web is however always open to students. Students can provide input into the course wiki (eg lecture notes and tips on useful readings), ask questions and discuss the course with other students. There is a moderator function that captures unanswered questions to the public agency KTH and sends them on to the proper authorities. You can find information about the course schedule aswell on the course web. More information about the course web.

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