Teaching programme 2009-2010

Autumn 2009: Bioinformatics - Computer science, mathematics and statistics - Biology and medicine
Spring 2010: Bioinformatics - Computer science, mathematics and statistics - Biology and medicine
Language courses
Teaching at departments
Location guide
Previous academic years

Teaching and event calendar

MBI teaching and event calendar gives teaching times for courses listed below as "Bioinformatics courses" (including some Computer science and Statistics courses which are recommended) and "Biology for methodological scientists" and "Measurement techniques" Note that you must include other courses from Biology and medicine, Computer science, Mathematics and Statistics, as well as Language studies in your personal calendar to meet the requirements. Links to other biology courses: Department of Biological and Environmental Sciences(Viikki) and Faculty of Agriculture and Forestry (Viikki)

Autumn 2009

Bioinformatics courses / Autumn 2009

This list includes the major courses. Note that some of them can also be included as minor subject studies in Computer science, Statistics, Biology.

582606 Introduction to Bioinformatics (4 credits, Compulsory)
University Lecturer Sirkka-Liisa Varvio, Tue, Thu 14-16 Exactum D122, Exercises Thu 16-18 Exactum (I period)
This course gives an introduction to the central topics in bioinformatics, and gives a foundation for further courses in the Master's Degree Programme in Bioinformatics (MBI). Course exam 21st of October from 16.00 to 19.00.
Placement: 1st year

T-61.5120 Computational genomics (4-7 credits)
Teaching Researcher Fabian Hoti, Fri 9-14 T-building room A328 (I-II periods)
Algorithms and models for biological sequences and genomics.
Placement: 1st year

582653 Computational methods of systems biology (4 credits)
Professor Esko Ukkonen, Tue, Thu 10-12 Exactum , Exercises Thu 14-16 Exactum (II period)
The course is an advanced introduction to computational methods for analysing genomic and gene expression data to find different functional units (such as genes) and regulatory structures and relations (such as gene enhancers).
Placement: 1st or 2nd year

T-61.5110 Modelling biological networks L (5-7 credits)
Professor Harri Lähdesmäki, Mon 10-14, Tue 10-12 T-building room A238 (I period)
Placement: 1st or 2nd year

57730 Sequence evolution from molecules to genomes (4 credits)
University Lecturer Sirkka-Liisa Varvio, Tue 14-18, Exactum B120 (II period)
This course can also be included as minor subject studies in biology by replacing bioinformatic exercises with biological essays.
Placement: 1st year

58307312 Master's thesis seminar
University Lecturer Sirkka-Liisa Varvio, Mon 16-17 Exactum room C220 (I-IV periods, Compulsory)
While working on the Master's thesis, the MBI student is expected to participate in the Master's thesis seminar on a regular basis and give two presentations, one on the research plan and the other on the (nearly) completed thesis. The Master's thesis seminar operates throughout the year.
Placement: 1st and 2nd year

57732 Seminar on statistical methods in bioinformatics (3 credits)
Senior Research Scientist Mikko J. Sillanpää, Thu 12-14, Exactum B120 (II period)
Placement: 2nd year

Programming in Python (4 credits)
Jarkko Toivonen, Exactum (I period)
This course is for minor subject studies in computer science.

Design and analysis of genome-wide association studies, fall 2009 (3 credits)
Adjunct prof. Samuli Ripatti, Computer class C128, Exactum.
Lectures: 2/12/2009(Wed),3/12/2009(Thu) and 5/12/2009(Fri), 09:00-16:00
This is an intensive course for advance studies.

Courses in biology and medicine / Autumn 2009

399672 Biology for methodological scientists (8 credits, Compulsory)
This course gives an introduction to basic concepts and techniques of molecular biology. The course is particularly tailored for students with no previous molecular biology background. The course consists of four modules, 2 credits each: Genetic analysis reading group(I period), Sequencing and microarrays (II period), Medical genetics and plunge into development biology (III and IV periods). Each module has its own homepage which includes the time schedule, registration, grading and examination information.
Genetic analysis reading group (2 credits)
Maral Jamshidi, and Sirkka-Liisa Varvio (I period).
Microarrays and next-generation sequencing (2 credits)
Henrik Edgren (II period).
The goal of this course is to give students an understanding of how microarray and next generation sequencing techniques work in the laboratory and what kind of biological problems they can be applied to. See course area in moodle for more details.
Placement: 1st year (I-IV periods)

399673 Measurement techniques (6 credits, Compulsory)
This lab course introduces students to molecular biology technologies. The course is particularly tailored for students with no previous molecular biology background. The course comprises six modules, which cannot be taken separately: How to work in the laboratory, Microarrays, Mass spectrometry, SNP genotyping, Cellular imaging, In situ hybridization. Each module has its own home page (links to be added here) which includes course content, schedule and contact details of teachers. There is no examination. An accepted performance of the course requires that the student takes part in all teaching sessions. Missing a session can be compensated by making a task given by the coordinator of the module.
How to work in laboratory, (Link to be added)
Ville Pulkkinen (I period)
Microarrays, (Link to be added)
N.N. II period.
Placement: I-IV periods, 1st year

Links to other biology courses: Department of Biological and Environmental Sciences(Viikki) and Faculty of Agriculture and Forestry (Viikki)

Courses in computer science, mathematics and statistics / Autumn 2009

Courses listed below are suitable for MBI minor subject studies. Other courses may be suitable as well.

Introduction to Statistics (10 credits)
Xiaoin Dong, Tue 8-10, U40 Room 7, Fri 10-12 in U40 Room 9, starting on September 15. U40 stands for Unioninkatu 40, Metsätalo. (I-II periods).
This course is for students with no previous studies in statistics.

Introduction to Programming (5 credits)
Assistant Professor Arto Wikla, and Henning Lübbers
A weekly teaching group for foreign students
Starts Monday September 7th, afterwards Mondays 12-14 and Thursdays 14-17 (Auditorium A111, Exactum)
This course is for students with no previous studies in computer science.

T-61.5060 Algorithmic Methods of Data Mining L (5 credits)
Academy Professor Heikki Mannila (II period)

Information-Theoretic Modeling (4 credits)
Teemu Roos, Lectures(Period I: 8.9-16.10 Tue & Fri 10-12, C222, Exactum), Exercises(15.9-13-10. Tue 12-14 B119 Exactum)

Project in Information-Theoretic Modeling (2 credits)
Teemu Roos, Exactum (II period)

Introduction to Bayesian methods and WinBUGS
J Ranta, 31.8.-11.9. Exactum B120

Introduction to Machine Learning (4 credits)
Hannes Wettig, Wed, Fri 12-14 Exactum C222 (II period)

T-61.3050 Machine Learning: Basic Principles (5 credits) (Place: TKK)
Starting September 7th, 2009. Lectures(wed and fri 10-12 in T2), Exercises (wed and fri 12-14 in T3 starting one week later) (I period)
Check course webpage for more information.

T-61.5130 Machine Learning and Neural Networks L (5 credits)
Professor Juha Karhunen (II period)

T-61.3040 Statistical Signal Modeling (5 credits)(Place: TKK)
D.Sc. (Tech.) Jaakko Peltonen (I-II periods)

Mathematics of infectious diseases (10 credits)
Postdoc Barbara Boldin (I-II periods)

Mathematical modelling (10 credits)
University lecturer Stefan Geritz (I-II periods)

T-61.5080 Signal processing in neuroinformatics (5 credits)
Adjunct Professor Ricardo Vigario, T-building room TBA (I-II periods)
The goal of the seminar is to give an overview of some of the main biomedical signal processing techniques, with clear emphasis to EEG and MEG.
Placement: 1st or 2nd year

Spring 2010

Teaching and event calendar

Bioinformatics courses / Spring 2010

This list includes the major courses. Note that some of them can also be included as minor courses in Computer science, Statistics, Biology.

582604 Practical Course in Biodatabases (4 credits, Compulsory)
University Lecturer Sirkka-Liisa Varvio, Thu, Fri 14-16 Exactum BK107, Exercises Thu 16-18 B221 (III period)
Techniques for accessing and integrating data in biological databases are studied. Prerequisities: Introduction to Bioinformatics, basic programming skills.
Placement: 1st year

57734 Modelling inheritance in pedigrees and populations (4 credits)
University Lecturer Sirkka-Liisa Varvio, Tue 14-18, Exactum B120 (III period)
This course can also be included as minor subject studies in Biology.
Placement: 1st year

58310108 Seminar: Sequence assembly (3 credits)
Adjunct Professor Veli Mäkinen, Mon 12-14 Exactum C222 (III-IV periods)
Placement: 1st or 2nd year

58310107 Seminar: Neuroinformatics (3 credits)
Professor Aapo Hyvärinen, Thu 12-14 Exactum C222 (III-IV periods)
Placement: 1st or 2nd year

58309309 Seminar: Gene regulatory networks (3 credits)
Professor Esko Ukkonen, Mon 14-16 Exactum C222 (III-IV periods)
Placement: 1st or 2nd year

57733 Computational statistics (10 credits)
University lecturer Petri Koistinen, Mon 12-14, Fri 12-14, Exercises Fri 10-12, Exactum B120 (III-IV periods)
This course can also be included as minor subject studies in Statistics.

T-61.5050 High-Throughput Bioinformatics (5-7 credits)
Jarkko Salojärvi, Tue 10-12, Exercises (TBA) Room T4, T-building, (III-IV periods), TKK
The course introduces computational and statistical methods for analyzing modern high-throughput biological data, in particular microarray data, and their use in systems biology. Necessary biological background is reviewed briefly.
Placement: 1st year

57710 Software tools for statisticians (2 credits)
R-course. University lecturer Petri Koistinen, Mon 10-12, Thu 10-12, C128 (III period, three first weeks)
This course is for minor subject studies in Statistics. Placement: 1st year

57729 Phylogenetic data analysis (6-8 credits)
University Lecturer Sirkka-Liisa Varvio, Tue 14-18, Exercises Thu 14-16, Exactum B120 (IV period)
Placement: 1st year

T-61.6070 Special course in bioinformatics I L (3-7 credits)
Professor Harri Lähdesmäki, Mon 12-14 room T4, Wed 10-12 NOTE: Wednesday may change to another day! Room T5, T-building (IV period)
Note: this course corresponds to a seminar course at HY.
Placement: 1st or 2nd year

Courses in biology and medicine / Spring 2010

399672 Biology for methodological scientists (8 credits, Compulsory)
Course continues from Autumn 2009 by modules III (III period) and IV (IV period).
Wednesdays in III and IV.
399672-3 Medical Genetics (III period) (20.01.2010-03.03.2010) (2 credits)
Elisabet Einarsdottir and Lotta Koskinen .
Deadline for registration 11.01.2010

399673 Measurement techniques for bioinformatics (6 credits, Compulsory)
Course continues from Autumn 2009.
Wednesdays in III and IV. There are also non-Wednesday sessions, see MBI teaching and event calendar

812010 Laboratory Course in Plant Molecular Biology (KBIOT401) (5 credits)
Professor Teemu Teeri, Professor Jari Valkonen
25.1-10.2.2010 at 9-16 (except on Mon and Thu at 12-16), Viikki C-building, course lab 144 (III period)
Relations to other study units: Basics in gene technology and plant molecular biology. Study materials and literature: Course manual. Evaluation: Laboratory report (pass/fail). Registration: via WebOodi.

81028 Laboratory Course in Plant Biotechnology (KBIOT301) (5 credits)
Professor Teemu Teeri, University Lecturer Mika Kotilainen
22.2.-.5.3.2010 at 13-18, 9.3.-11.3.2010 at 13-18, 16.3.2010 at 13-18, 18.3.2010 at 13-18, 24.3.2010 at 13-18, 7.4.2010 at 13-18, 20.4- 21.4.2010 at 13-18 (III-IV periods)
Place: Viikki C-building, course lab 144 (except 22.2-26.2.2010 in Biocenter 1, course lab 1026)
Relations to other study units: 81085 Plant Biotechnology and Molecular Biology (KBIOT300) lectures. Study materials and literature: Course manual and scientific articles. Evaluation: Laboratory report (pass/fail). Registration: via WebOodi. Other information: The course is given jointly by the Faculty of Agriculture and Forestry and the Faculty of Biosciences.

Other biological courses can be taken from:
Department of Biological and Environmental Sciences(Viikki)
Faculty of Agriculture and Forestry (Viikki)

Courses in computer science, mathematics and statistics / Spring 2010

Courses listed below are suitable for MBI minor subject studies. Other courses maybe be suitable as well - discuss with your student counsellor!

58310111 Seminar:Graph Mining (3 credits)
Prof Hannu Toivonen, and Dr S Mahler, Exactum C220
Note the special timings of seminar at course webpage.

582456 Approximation Algorithms (8 credits)
Jyrki Kivinen, Exactum (III-IV periods)

582634 Data Mining (4 credits)
Dino Pedreschi, Exactum (IV period)

582635 Data Mining Project (2 credits)
Dino Pedreschi, Exactum (IV period, intensive phase)

582636 Probabilistic Modeling (4 credits)
Petri Myllymäki, Tue, Thu 16-18 Exactum B222 (III period)

582637 Project in Probabilistic Modeling (2 credits)
Hannes Wettig, Thu 16-18 Exactum (IV period)

58131 Tietorakenteet (Data Structures, lectured in Finnish) (8 credits)
Patrik Floréen, Tue, Thu 10-12 Exactum A111 (III-IV periods)
This course is for students requiring supplementary studies in computer science.

582638 Unsupervised Machine Learning (4-6 credits)
Aapo Hyvärinen, Tue, Thu, Fri 14-16 Exactum C221 (IV period)

582601 XML-tietokannat (XML Databases, lectured in Finnish) (4 credits)
Miro Lehtonen, Exactum (IV period)

T-61.5090 Image Analysis in Neuroinformatics (5 credits)
Adjunct Professor Ricardo Vigario, T-building (III-IV periods)
The goal of the seminar is to give an overview of some of the main biomedical signal processing techniques, with clear emphasis to neural data. Topics range from artifact removal and image enhancement to pattern classification and diagnostic decision.
Placement: 1st or 2nd year

Stochastic methods in physics and biology (10 credits)
University lecturer Stefan Geritz (III-IV periods)

Delay equations (10 credits)
Professor Mats Gyllenberg (III-IV periods)

Language courses

993734 Academic Writing for Students in English-Medium Master's Degree Programmes 1 (2 credits, compulsory)
Autumn 2009
Teachers: R. Siddall
Place: Viikki
Times: Fridays 10-14, I period
Aim: The aim of this course is for students to achieve a high level of academic English required for completing study-related academic texts (e.g. theses, reports, essays, academic articles).

993735 Academic Writing for Students in English-Medium Master's Degree Programmes 2 (2 credits, compulsory)
Autumn 2009
Teachers: K. Pitkänen
Place: Exactum
Times: Fridays 10-14, II period
Aim: The aim is to improve the student's academic writing skills and provide consultation, feedback and language support for writing a high quality thesis in English. The focus is on editing draft versions of the thesis based on the feedback received during the consultation sessions. Poster writing and oral presentation of research are also covered.

Academic Writing courses are organized by the Language Support for English-Medium Master's Programmes project.