Department information

 

Sub-programme on bioinformatics and computational biology

Modern biological sciences are based heavily on computational methods. Molecular biology, genetics, and ecology, for instance, require fairly complicated computational methods, and new methods are constantly needed. The sub-programme on bioinformatics and computational biology educates developers of such methods, and specialists on managing and processing biological data. The sub-programme is related methodologically to the specialization areas on algorithms, information management, and intelligent systems. The focus of studies can be flexibly tuned between data analysis and bioinformatics.

Graduates are employed as experts of computational methods in research institutes and companies.

Research areas during 2005-2006:

• Algorithms of structural and systems biology (Esko Ukkonen, Juho Rousu)
• Computational methods of gene mapping (Hannu Toivonen, Heikki Mannila)
• Algorithmic questions about genome structure (Heikki Mannila, Esko Ukkonen, Marko Salmenkivi)
• Gene expression data analysis (Samuel Kaski)
  
• Neuroinformatics (Aapo Hyvärinen, Jarmo Hurri, Patrik Hoyer)

See additionally Bioinformatics at the University of Helsinki.

Teaching in 2005-2006

In Autumn 2005, the following lecture courses will be given:

• Introduction to Bioinformatics, 6 cu (Mäkinen)
• Molecular genetics and gene mapping for methodological sciences,  2ov (Onkamo) NOTE: origanized summer 2005, not autumn
  
• Biological sequence analysis, 6 cu (Ukkonen)

and the following seminar:

• Metabolic Modeling, 3 cu (Rousu)

In Spring 2006, the following lecture courses will be given

• Computational systems biology, 6 cu (Rousu, Holm)
• Modelling of vision, 5 cu (Hyvärinen)

and the seminar

• Seminar on biological sequence analysis and comparative genomics, 3 cu (Ukkonen)

Teaching in 2005-2006 at other locations

Also other Faculties, and Helsinki University of Technology (HUT), organize courses on the field. For example, the following courses are recommended:

• High-throughput bioinformatics (Kaski, HUT)
• Analysis of proteomic and metabolic data (Kaski, Oresic, HUT)
• Biology for methodological scientists, 8 op (Faculty of Medicine, January 2006->)
• Practical Bioinformatics, 8 op (Faculty of Medicine, November 2005->)

Degree requirements

Sub-programme on bioinformatics and computational biology (95 cu)

1. Major subject studies

CUM LAUDE in COMPUTER SCIENCE

• 582313 Introduction to Bioinformatics, 6 cu (if not already included in the Cum laude studies)

584326 ADVANCED SPECIAL STUDIES

• Mandatory studies in the specialization area, 12 cu
  • Gene sequence studies, 6 cu
  • 582469 Computational systems biology, 6 cu (During academic year 2006-2007, the course "582469 Computational Systems Biology" can be taken by a separate exam or alternatively by taking the courses "582605 Metabolic modeling" and "582612 Practical course in microarray data analysis".)
• Elective studies in the specialization area, 14 cu
  • Specialization area maintains a list of recommended courses in its web-page (see below)
• Seminars, 6 cu
• Elective computer science advanced special studies courses (other than seminars), 8 cu
• 50131 Master's thesis, 40 cu
• 50039 Kypsyysnäyte

2. Minor subject studies

Minor subjects should be chosen so that they, together with the minor subjects included in the Bachelor's degree, fulfil one of the alternatives:

Mathematics or extended minor studies module on methodological sciences (50 cu) and minor studies module on Biology or on other suitable subject (25 cu)
OR
Mathematics or minor studies module on methodological sciences (30 cu) and extended minor studies module on Biology or on other suitable subject (50 cu).

Individual choices must be negotiated with the Professor in charge of the specialization area.

3. Other studies

• 582510 Personal study plan (FM-HOPS), 1 cu
• 584403 Practical training, 2-6 cu
  • 582511 Working experience in demanding information technology posts (2-6 cu) OR
  • 581387 Tietotekniikka: Nyt! (3 cu) or some other suitable course
• Elective studies

Recommendations

Bioinformatics graduates should acquire firm skills in mathematics and statistics, and basic knowledge in biology. An advanced course in at least one branch of bioinformatics should be taken. After acquiring this strong basis it is possible to flexibly choose the focus of studies in between data analysis and bioinformatics, and to specialize on either one subfield of computer science or gain general knowledge of several subfields.

Biological background can be studied either as a minor subject, or in special courses tailored to students of methological sciences.

Focus of specialization in methods of computer science will be chosen by selecting a suitable set of courses from the other specialization areas.

Finally, special skills will be acquired in bioinformatics special courses and seminars, and the skills will be applied to bioinformatic research problems in the Master's thesis.

Exceptions to the recommendations below are allowed only for good reasons.

Minor subjects

Strong minor module in mathematics and statistics is strongly recommended, as well as in some biological science. For instance the following combination is suitable (Availability in English will be checked later. Some credit units below follow the old system, hence marked with ov):

• Minor module in methodological sciences (cum laude, at least 35 ov)

• Matemaattiset apuneuvot I ja II, 10ov
• Diskreetti matematiikka, 5ov
• Todennäköisyyslaskenta I, 5ov
• Johdatus todennäköisyyslaskentaan ja tilastotieteeseen, 6ov (or Tilastotieteen jatkokurssi, 6ov)
• The rest according to interests

Professor in charge

during 2005-2006 is. Juho Rousu.

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Last updated September 15, 2005, by Veli Mäkinen.