Uusi opinto-opas (sisältäen myös opetusohjelmat) lukuvuodelle 2018-2019 sijaitsee osoitteessa https://opas.peppi.utu.fi . Tältä sivustolta löytyvät enää vanhat opinto-oppaat ja opetusohjelmat.

The new study guide (incl. teaching schedules) for academic year 2018-2019 can be found at https://studyguide.utu.fi. This site contains only previous years' guides.

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Arkistoitu opetusohjelma 2016–2017
Selaat vanhentunutta opetusohjelmaa. Voimassa olevan opetusohjelman löydät täältä.
BKEM1050 In Silico Methodologies in Biochemistry and Molecular Medicine 5 ECTS
Periods
Period I Period II Period III Period IV
Language of instruction
English
Type or level of studies
Advanced studies
Course unit descriptions in the curriculum
Biokemia
Department of Biochemistry

Learning outcomes

After a successful completion of this course, students will have
1. Obtained an appreciation of the quantitative aspects of analyzing scientific (big) data either stored in large data databases or generated by sophisticated modeling and simulation tools.
2. Gained a basic understanding of applying various bioinformatics methods to large biological data sets.
3. Realized the potential of scientific computing for the study of the behavior of biological systems, in particular large biological macromolecules.

General description

This course aims at emphasizing the quantitative aspects of scientific research. For this, the course contains three intertwined components: (i) searching and evaluating nucleic acid and protein structural data from various databases, (ii) use of scientific computing to study structural, dynamical, functional and thermodynamical properties of proteins and membranes and their interaction with other molecules, and (iii) using biocomputing tools to access and analyze large and high-throughput data produced and accessible through biochemical and computational experiments.
Students will learn to access biological databases, search and retrieve relevant data, analyze data in a meaningful manner, and link data and results obtained from different tools. A very brief introduction to metabases and data compilation is provided as well. Interaction studies are emphasized through genome-wide mapping of protein-DNA interaction, proteomics-based bioinformatics, and high-throughput mapping of protein-protein interaction networks. Commonly employed modeling and simulation techniques will also be dealt with. These include molecular dynamics, Monte Carlo and Langevin (stochastic, Brownian) dynamics, continuum electrostatics, statistical thermodynamics, protein modeling techniques, protein-ligand docking, protein-ligand affinity calculations and the computer simulation of the protein folding process and enzyme action.

Teacher responsible

Pekka Rappu

Teaching

7-Nov-2016 – 16-Dec-2016
Lectures 32 h
Mon 7-Nov-2016 - 21-Nov-2016 weekly at 12-14, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Tue 8-Nov-2016 - 22-Nov-2016 weekly at 12-14, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Wed 9-Nov-2016 - 23-Nov-2016 weekly at 10-12, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Thu 10-Nov-2016 at 12-14, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Fri 18-Nov-2016 - 25-Nov-2016 weekly at 14-16, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor, CANCELLED!
Wed 7-Dec-2016 at 11-13, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Thu 8-Dec-2016 at 11-13, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Fri 9-Dec-2016 at 11-13, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Wed 14-Dec-2016 at 8-10, ARC A250, Kurssityökirjoitustila, Arcanum 2nd floor
Exercises 40 h
Mon 28-Nov-2016 at 12-16, ARC IT-luokka A252, 2.krs
Tue 29-Nov-2016 at 12-16, Publicum IT-luokka PUB409
Wed 30-Nov-2016 at 12-16, ARC IT-luokka A252, 2.krs
Thu 1-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Fri 2-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Mon 12-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Tue 13-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Wed 14-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Thu 15-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs
Fri 16-Dec-2016 at 12-16, ARC IT-luokka A252, 2.krs

Evaluation

Pass/fail.

Further information

All lectures and exercises are broadcasted via remote connection from University of Oulu, Finland.