Systems Biology

Bioinformatics MRes module, 2007-2008

Module home page: www.brc.dcs.gla.ac.uk/~drg/courses/sysbiomres

David Gilbert [drg@brc.dcs.gla.ac.uk]

Systems Biology - module introduction
The amount and variety of biological data now available, together with techniques developed so far have enabled research in Bioinformatics to move beyond the study of individual biological components (genes, proteins etc) albeit in a genome-wide context to attempt to study how individual parts cooperate in their operation. Bioinformatics as a scientific activity has now moved closer to the area of Systems Biology which seeks to integrate biological data as an attempt to understand how biological systems function. By studying the relationships and interactions between various parts of a biological system it is hoped that an understandable model of the whole system can be developed.

Module contents

Basic concepts of Systems Biology
Techniques and tools to
- model biochemical networks,
- store and visualise these models and associated data,
- simulate and analyse the behaviour of biochemical networks.
Illustrative examples
- metabolic networks
- gene regulation networks
- signal transduction networks
- protein-protein interaction networks
- developmental networks

Related course readings Advanced Research Readings in Computer Science - Bioinformatics and Systems Biology (campus access only).

Timetable: Term 2, 2007-2008.
Friday 22nd February, Graham Kerr Seminar Room 10:30 till 11:30,
Lab room 101 Davidson Building 11:00 till 12:00 or 12:00 till 1:00
LAB TIME STILL TO BE CONFIRMED FOR THIS SESSION

Wednesday 27th February, Boyd Orr Room 831, 10:00 till 11:00
Lab room 101 Davidson Building, 2:00 till 3:00

Thursday 28th February, Graham Kerr Library, 10:00 till 11:00
Lab 1 room 101 Davidson Building, 1:30 till 2:30

Friday 29th February, Bioinformatics Research Centre, Joseph Black Building, 10:00 till 11:00
Lab room 101 Davidson Building, 11:00 till 12:00

Course staff
Course lecturer: Professor David Gilbert
Course demonstrator: Xu Gu
Computing systems support officer: Robin Donaldson

Prior knowledge: The preceeding lectures in the Bioinformatics MRes course, and a basic background in biochemistry.

Slides / handouts

Session/Date	SLIDES	TUTORIAL	COURSEWORK
1: 22 Feb	Systems Biology: Introduction	Lab 1, Lab 1 extra - textmining
2: 27 Feb	Networks: representation & static analysis	Lab 2
3: 28 Feb	Modelling dynamic behaviour	Lab 3 (Xu Gu)
5: 29 Feb	Modelling dynamic behaviour	Lab 4; extra! :- BioNessie and MC2 Snoopy - Petri net tool	Coursework

Readings and Course texts :

Broder S, Venter J C, Whole genomes: the foundation of new biology and medicine, Curr Opin Biotechnol. 2000 Dec;11(6):581-5.
Kitano H. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. Curr Genet. 2002 Apr;41(1):1-10.
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science. 2002 Oct 25;298(5594):824-7.
Yuri Lazebnick. Can a biologist fix a radio? - Or, What I learned while studying Apoptosis. Cancer Cell september 2002 vol 2 179-182.
Post Genome Informatics Kanehisa. Publisher OUP. Year 2000. Isbn 0198503261. Category background

On-line resources:

http://www.brc.dcs.gla.ac.uk/~drg/bioinformatics/resources.html
Bioinformatics educational resource at the European Bioinformatics Institute.
International Society for Computational Biology www.iscb.org - very good rates for students, and you get on-line access to the Journal of Bioinformatics.