Bioinformatics – (M.Sc.)

Contents

Preliminary list of courses
Personal mentor
All students will have personal mentor to help them with their studies.
Schedule and courses
Most students will follow the following program

Fall year 1:
Introductory course, 5 weeks
Bioinformatics course, 5 weeks

The amount of available data in life sciences is rapidly increasing. and to use this data in the best possible way is rapidly becoming one of the corners stones in all biological research. 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. In this course we will cover the basic bioinformatical methods to analyze protein sequence and protein structure. The goals are that 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

Comparative Genomics, 5 weeks
Today the genome sequence of hundreds of organisms is known, including our own genome sequence and that of many closely related species. To understand human origin as well as how life in general has evolved it is necessary to compare these genomes. In this course you will learn how to compare genomes. You will learn the basic methods of phylogeny and orthology prediction as well as other methods to understand the evolution of genes and genomes.

Molecular Modeling, 5 weeks
Modeling of biological systems at the molecular level is becoming increasingly important. In this course we will provide an introduction to methods that are used to in molecular modeling. Both methods using quantum mechanical descriptions and classical descriptions will be discussed. Methods that will be discussed include: Coordinate systems, molecular graphics, hartree-fock, basis sets, semi-empirical methods, Density Function Theory, Molecular Mechanics, Energy Minimization, Molecular dynamics simulations, Monte Carlo methods. Sequence Alignments

Spring year 1:
Biological membranes or Molecular properties of proteins, 10 weeks

Protein Physics, 5 weeks
This is an advance level course in collaboration between Stockholm University and KTH that covers structure, self-organization, and function of the biological macromolecules of life - primarily proteins. It will cover biophysical chemistry of proteins folding, Protein structure, Protein Folding and Protein structure prediction.

Membrane and globular protein structure prediction, 5 weeks
In this course we will use (and develop) state of the art methods to predict the structure of globular and membrane proteins. In particular we will focus on the structure prediction CASP process and analyze how we can solve one of the hardest problems in biology today, the possibility to predict a protein structure from its sequence. The course consist of three parts, lectures describing different methods for structure prediction, a literature assignment of CASP papers and a project aimed at the development of an improved structure predictor. The course is based on weekly seminars and assignments during one semester.

Year 2

Applied scientific programming, 3 weeks
This is a course aimed at improving your efficiency as a bioinformatician. Here we will teach you practical methods that are needed to a) rapidly produce functional bioinformatical code, using tools such as Bio-PERL and related projects.b) Optimally optimize your code for modern computer architectures. Here the focus will be how to best use the rapid advances in multi-core CPUs as well as the high performance of modern graphics cards.

Project work 20 to 40 weeks
Electable courses for 0 to 20 weeks, possible choices include
Computational Biochemistry
Structural biochemistry
Algorithmic bioinformatics
Machine learning
Modeling of cell-biological processes
Computational Physics