Computational Systems Biology

Course provider:
The University of Manchester

Course contact:
Pedro Mendes (pedro.mendes@manchester.ac.uk)

Summary:
This course aims to ensure that the successful student understands mathematical representations of biochemical networks, the computational methods to simulate them, and the software used. By the end of the course s/he will be able to construct a computational model of a biochemical network, to study a given computational model of a biochemical network in terms of its dynamics and be able to calibrate biochemical models given a set of experimental data. It is an advanced module from our theme in Computational Systems Biology, designed to follow :
Bioinformatics for Systems Biology
Mathematics for metabolic modelling

Syllabus:
This module will provide an introduction to the computational methods for analysis and simulation of biochemical networks. It will cover :

mathematical representations of biochemical networks;

simulation of the dynamics of biochemical models using differential equations and stochastic methods;

analysis of the structural properties of biochemical networks;

analysis of the steady state control properties of biochemical networks;

calibration of biochemical models through parameter estimation techniques;

operation and interoperation of software for systems biology.

Assessment:

The assessment methods are shown below.

There will be an assessed tutorial exercise for each section of the course. These exercises will be brief: they are included as one means of maintaining a dialogue between all those participating in the course.

There will be two further written assessments. At the discretion of the examiners, you may also be required to attend a viva voce examination.

Further details:
All the course materials are provided within the Moodle virtual learning environment (VLE). The tools provided will allow you to navigate and search through the course textbook, practical exercises and references to other useful texts and URLs. The course 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 the members of the course team, and with other learners, through course bulletin boards. Our students and graduates can 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.

References:
tbc

Course provider:	The University of Manchester
Course contact:	Pedro Mendes (pedro.mendes@manchester.ac.uk)
Summary:	This course aims to ensure that the successful student understands mathematical representations of biochemical networks, the computational methods to simulate them, and the software used. By the end of the course s/he will be able to construct a computational model of a biochemical network, to study a given computational model of a biochemical network in terms of its dynamics and be able to calibrate biochemical models given a set of experimental data. It is an advanced module from our theme in Computational Systems Biology, designed to follow : Bioinformatics for Systems Biology Mathematics for metabolic modelling
Syllabus:	This module will provide an introduction to the computational methods for analysis and simulation of biochemical networks. It will cover : mathematical representations of biochemical networks; simulation of the dynamics of biochemical models using differential equations and stochastic methods; analysis of the structural properties of biochemical networks; analysis of the steady state control properties of biochemical networks; calibration of biochemical models through parameter estimation techniques; operation and interoperation of software for systems biology.
Assessment:	The assessment methods are shown below. There will be an assessed tutorial exercise for each section of the course. These exercises will be brief: they are included as one means of maintaining a dialogue between all those participating in the course. There will be two further written assessments. At the discretion of the examiners, you may also be required to attend a viva voce examination.
Further details:	All the course materials are provided within the Moodle virtual learning environment (VLE). The tools provided will allow you to navigate and search through the course textbook, practical exercises and references to other useful texts and URLs. The course 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 the members of the course team, and with other learners, through course bulletin boards. Our students and graduates can 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.
References:	tbc

Distance learning in computational biology Courses in computational biology

Updated 18 March 2011 by Heather Vincent