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University of Helsinki / Department of Computer Science / Copyright © 2008 Jan Lindström.

Updated 25.03.2008

58308110 Seminar: Management of Biological Databases (3 cu), spring 2008

17.01.--21.02. Th 10--12 C220, 13.03.-24.04. Th 10--12 C220 Instructor: Jan Lindström, PhD

Overview.

As of 2006, there are over 1,000 public and commercial biological databases. These biological databases usually contain genomics and proteomics data, but databases are also used in taxonomy. The data are nucleotide sequences of genes or amino acid sequences of proteins. Furthermore information about function, structure, localisation on chromosome, clinical effects of mutations as well as similarities of biological sequences can be found.

Biological databases have become an important tool in assisting scientists to understand and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species. This knowledge helps facilitate the fight against diseases, assists in the development of medications and in discovering basic relationships amongst species in the history of life.

The biological knowledge is distributed amongst many different general and specialized databases. This sometimes makes it difficult to ensure the consistency of information. Biological databases cross-reference other databases with accession numbers as one way of linking their related knowledge together.

An important resource for finding biological databases is a special yearly issue of the journal Nucleic Acids Research (NAR). The Database Issue of NAR is freely available, and categorizes many of the publicly available online databases related to biology and bioinformatics.

In this seminar, we cover topics related to biological database management.

Prerequisites.

All participants must have a bachelor's degree or have passed the Scientific Writing course. Background in basic database management is required. Knowledge about biological databases is a plus, but not required.

Structure of the Seminar

The language of the seminar is English.

To pass the seminar, you need to do the following four tasks:

During Period I all students write their papers in English. The length of the paper is 6-10 pages formatted according to the IEEE Transactions guidelines. The oral presentations, during Period II, should last for about 30-35 minutes, which should leave some time for questions.

IEEE guidelines for the paper (Latex and Word) can be found from the IEEE Transaction author guide: http://www.ieee.org/pubs/authors.html.

Schedule

Grading

Students will be graded based on i) their written paper (40%), ii) their oral presentation (40%), and iii) their activity in commenting other students' work and participating in the discussion (20%). To pass the course, the student must write the paper on the agreed subject and present his work. In addition, each student is required to attend at least 80% of the seminar presentations.

List of possible topics

Links


Jan Lindstrom (Jan.Lindstrom@cs.Helsinki.FI)

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