Overview of classic and modern high-throughput methods for sequencing DNA and analysis of proteins with mass spectrometry. Methods for gene and genome assembly from DNA data. Mapping of short DNA reads to a genome for further analysis of genome variation and gene structure. Techniques for analysis gene structure and activity.
Identification and quantification of proteins given mass spectrometry data.
DD2399 Omic Data and Systems Biology 7.5 credits
This course has been discontinued.
Last planned examination: Spring 2018
Decision to discontinue this course:
No information inserted
Course offerings are missing for current or upcoming semesters.
Headings with content from the Course syllabus DD2399 (Spring 2013–) are denoted with an asterisk ( )
Content and learning outcomes
Course contents
Intended learning outcomes
The students should after the course
- be able to discuss modern high-throughput methods with biologists,
- know current public databases well enough to be able to evaluate the feasibility of a project,
- be able to use popular tools for analysis of omics data as wells as explain and discuss the relative benefits of these,
- be able to give intuitive descriptions of algorithms and methods for analysis of omics data as well as, using the course literature, immediately implement those.
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
Bioinformatics corresponding DD2397/DD2404 Applied Bioinformatics.
Computer science corresponding to DD1339/DD1340/DD1341 Introduction to Computer Science or DD1320/DD1321 Applied Computer Science. Probability theory corresponding to SF190 Probability Theory and Statistics.
Equipment
No information inserted
Literature
To be announced at the web page for the course at least 4 weeks before the course starts.
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 Work, 7.5 credits, grading scale: A, B, C, D, E, FX, 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.
Other requirements for final grade
Three laborations.
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
Education cycle
Second cycle
Add-on studies
Please discuss with the instructor.
Contact
Lars Arvestad, e-post: arve@kth.se