Courses of the Bioinformatics Master

Fall year 1:

  • Bioinformatics, KB7004, 7.5 ECTS Course page
    Arne Elofsson
    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, and Homology modeling.

  • Structural biochemistry, KB7002, 7.5 ECTS Course page
    Martin Högbom
    The course covers basic concepts in structural biochemistry and the experimental methods used to determine biological macromolecules at the molecular level. The course also deals with the relationship between structure and function from a molecular perspective and how the structural knowledge has increased our understanding of important biological processes.

  • Molecular Modeling KB8005, 7.5 ECTS Course page
    Erik Lindahl
    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.

  • Applied bioinformatics DA7021, 7.5 ECTS Course page Course page 2010
    Lars Arvestad
    This is a course aimed at improving your efficiency as a bioinformatician. Here you will learn practical methods that are needed to produce good bioinformatical code, using tools such as Bio-Python and related projects.

Spring year 1:

Period A-B:
  • Protein Physics KB8011, 7.5 ECTS Course page
    Erik Lindahl
    This is an advanced 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 covers the biophysical chemistry of protein folding, denaturation, stability and function.

    • Analysis of Data from High-throughput Molecular Biology Experiments BB2490, 7.5 ECTS
      Olof Emanuelsson and Lukas Käll
      This is an advanced course in bioinformatics. The course contains the fundamentals of bioinformatics analysis of large-scale data sets from genomics and proteomics experiments (in particular, DNA sequencing and mass spectrometry). The course consists of lectures and computer-based laboratory exercises.

      or

      Omic Data and Systems Biology DD2399, 7.5 ECTS
      Lars Arvestad
      Modern high-throughput biology methods; popular tools for analysis of omics data; algorithms and methods for analysis of omics data as well as their implementation.

Period C (21/3-1/5):
  • Structure Prediction of Globular and Membrane Proteins KB8008, 7.5 ECTS Course page Course page
    Arne Elofsson
    In this course we use (and develop) state of the art methods to predict the structure of globular and membrane proteins. In particular we focus on the structure prediction CASP process and analyze how we can solve one of the hardest problems in biology today, predicting 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.

Period D (2/5-5/6):
  • Comparative Genomics KB8007, 7.5 ECTS Course page
    Erik Sonnhammer
    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 biology and orgins 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 using bioinformatical techniques such as phylogeny and orthology prediction as well as other methods to understand the evolution of genes and genomes. Moreover, you will learn how to do functional annotation of proteins on the genome scale, and how to analyse the interactome.

Year 2