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|Notices (updated 23.12.2005)
o Project work data and information available
o The list of researchers worth checking in Literature section
|Lecturers||Prof. Sami Kaski, Laboratory of Computer and Information Science,|
Doc. Matej Oresic, VTT Systems Biology and Bioinformatics
|Assistant||M.Sc. Janne Nikkilä, Laboratory of Computer and Information Science|
|Semester||Autumn 2005 (during periods I and II)|
|Seminar sessions|| On Tuesdays at 14-16 in lecture hall T4 in computer science building,|
Konemiehentie 2, Otaniemi, Espoo. The first session on 13.9.2005.
|Registration||TKK students: WebTopi, others: send mail to email@example.com|
So far the most visible research effort in bioinformatics has been targeted on gene sequences and gene expression measurements (treated on the course T-61.5050). However, the key players controlling the cellular signalling and regulatory pathways are the proteins, products of gene expression. Another important class of molecules are the metabolites that are produced in most of the chemical reactions in the cell, and are key players in controlling the dynamics of the cell and intercellular communication. The measurement techniques to obtain data about these molecules in the cell are developing at an increasing pace, and the analysis of the data obtained is becoming more and more challenging, while also offering new opportunities for bioinformatics research.
This course is designed to introduce computational and statistical concepts and tools necessary to analyse data sets from various proteomic and metabolic data sources, in order to use them for life science and biomedical research.
The course participants have a possibility to visit Biotechnology laboratory in VTT in Otaniemi. The timetable will be fixed on 27.9.
This course is intended mainly for graduate students of computer science, statistics, and applied mathematics, but students from other fields are welcome as well. In particular mathematically oriented biology, bioinformatics, and medical students should benefit from the course.
Basic knowledge of probability, statistics, vector algebra, and calculus is assumed (the basic mathematics courses in HUT). A "Basic course in bioinformatics", such as S-114.2510 Computational Systems Biology or equivalent background is assumed as well.
Journal club (presentation + questions + project work) (5 cr).
The course is graded as fail/pass/pass with distinction. The exercises are graded as fail/pass (some percentage of the exercises is required with 'pass' to pass the course).
Make a presentation about a subject given in the first session.
Read each article to be presented in advance and make one question about it. The question should be the most relevant one in your opinion and one that should be answered in the presentation. Send your question a day before the presentation to the assistant. The questions are browsed after each presentation to make sure that each of them was relevant and was answered.
Complete the project work and return a written report about it.
Attend the seminar session and the discussion actively.
|HUT students:||In Webtopi|
|Other universities:||Send email to the organizers or sign up at the introduction lecture.|
Introductory material (read before 20.9.2005):
Researchers and research groups worth checking:
|Time||Lecturer||Subject and material|
|13.9.||Sami Kaski, Janne Nikkilä|
|18.10.||Laxman Rao Yetukuri|
|NOTE!!!: 3.11. 12.15 in A328||Vibhor Kumar|
|15.11.||Jarkko Ylipaavalniemi, Leena Hallivuori|
|29.11.||Laura Pombo, Ilana Saarikko||
In short: borrow the data dvd, copy the data, use MZmine to preprocess it, make an analysis, and write a report. DL is 15.1.2006. For more details, see the separate page.
For more information, please send email to firstname.lastname@example.org.
Sami Kaski, Matej Oresic, Janne Nikkilä
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