Bioinformatics for Systems Biology - a course in network biology using Cytoscape

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The October 2012 course is now full.



Course provider:
University of Manchester
Heather Vincent (
This introductory bioinformatics course is suitable for those with a first degree in either a biological science or in computer science. It covers the range of different datatypes now available for model building, such as transcriptome data. It could be taken as an individual short course, for professional development, and could be followed by one of more units from our theme in Computational Systems Biology :-

Mathematics for metabolic modelling
Computational Systems Biology
Bioinformatics for transcriptomics.

For those progressing to a Masters degree, it could lead to a research project in network biology.

This module will provide an introduction to the datatypes and modelling methods for network biology. It will cover :
  • the use of models in biology;
  • the structure and use of public pathway and interaction databases;
  • the reconstruction of biological networks from experimental data;
  • network statistics;
  • the analysis and interpretation of experimental data in the context of biological networks;
  • advanced topics.
The final section will prepare participants for the our advanced module in 'Computational Systems Biology'.


The assessment methods:

  1. There will be a tutorial exercise for each of the above topics.  These exercises will be brief: they are included as one means of maintaining a dialogue between all of our bioinformatics students. This exchange is particularly important for bioinformatics, which spans traditional academic disciplines.
  2. The main assessment will be a data analysis project and report.  At the discretion of the examiners, you may also be required to attend a viva voce examination.
Further details:
If you do not have much previous experience with the main bioinformatics services, databases and software, you might find it useful to prepare yourself by working through 'A practical guide to Bioinformatics' in EMBER. This is a very useful self-study introduction to bioinformatics. Please let me know if you have any problems in accessing EMBER.

All the learning materials that you need will be provided within the Moodle Virtual Learning Environment (VLE). The tools provided will allow you to navigate and search through the specially written textbook, practical exercises in biopinformatics and references to other useful texts and URLs. The textbook is provided as a set of web pages. It will be used to provide the necessary background to the focus of the course, which is problem-based learning.
You will interact with your tutor, and with other learners, through bulletin boards. Our students and graduates can continue to use the programme bulletin boards after a course has ended, so we now have a large and supportive online community.

Technical requirements:
This module is entirely web-based, so a reliable internet connection is essential. You will need access to a computer with at least 2 Gb of RAM. We will be using Cytoscape for some of the practical exercises, so you will also need Java version 5 or 6. Instructions on downloading and installing software are provided within the VLE.
An online textbook, and recommendations for additional reading, are provided within the Virtual Learning Environment. Additional textbooks, which will be useful for background reading, are:

Lawrence E. Hunter
The Processes of Life: An Introduction to Molecular Biology
MIT Press
ISBN-13: 978-0262013055

The above book, written for computer scientists, will be a useful reference text for many of our bioinformatics courses.

Klipp, Edda et al.
Systems Biology : a textbook
Wiley-VCH, 2009
ISBN: 3527318747, 9783527318742

Newman, M.E.J.
Networks: An Introduction
Oxford University Press, 2010
ISBN: 0199206651, 9780199206650

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Updated 13 September 2012 by Heather Vincent