Bioinformatics
The amount of available data in life sciences is rapidly increasing. To use this data in the best possible way, is rapidly becoming one of the corner-stones in all biological research. The course cover the basics of bioinformatics, especially methods to study biological sequence data and sequence statistics.
This course is part of the joint master’s programme in Molecular techniques in life science, together with KTH and KI. The course is not open for application to students outside of the programme.
In the future, or already today, we believe it will only be possible to become a successful life science scientist if you, in addition to your own data, fully can use data available from large scale studies.
This course will cover basic bioinformatical methods to analyze protein sequence and protein structure. After this course you should be able to use state of the art methods to predict the function and structure of an unknown protein sequence.
You will learn to use and understand the basic tools in bioinformatics, including tools for:
- Sequence searching
- Sequence alignments
- Secondary structure
- Fold recognition
- Homology modeling
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Course structure
The course deals with the basics of bioinformatics, especially methods for studying biological sequence data and sequence statistics.
After completing the course, the student is expected to be able to:
- Describe, explain, and compare basic methods for aligning sequences and searching sequence databases
- Explain and compare sequences, explain, and analyze methods for predicting properties of proteins
- Use Linux for standard tasks
- Demonstrate proficiency in solving problems using bioinformatics tools within given time frames
- Have an understanding on how machine learning works and how it is used in bioinformatics
Teaching format
Teaching consists of lectures and computer labs.
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Schedule
The schedule will be available no later than one month before the start of the course. We do not recommend print-outs as changes can occur. At the start of the course, your department will advise where you can find your schedule during the course. -
Course literature
Note that the course literature can be changed up to two months before the start of the course.
Pevsner, J., Bioinformatics and Functional Genomics (2009) John Wiley & Sons, Inc.
Other material will be given out during the course. These websites will be used as well:
3blue1brown.com/topics/neural-networks
neuralnetworksanddeeplearning.com
scikit-learn.org/stable/tutorial
carpentries-incubator.github.io/ml4bio-workshop
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Contact
Course coordinator and examinerArne ElofssonProfessor
Chemistry Section & Student Affairs Office- Visiting address
Arrhenius laboratory, room M345
Svante Arrhenius väg 16 A-D
- Here you will find:
Student administrator
International coordinator
Study advisor
Director of studies
- Office hours
Monday, Tuesday and Wednesday 09.00-11.30 and 12.30-15.00
- Phone hours
Wednesday 10.00-11.30 and 12.30-15.00
