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Team:Manchester/Collaboration
From 2013.igem.org
Our team believes that modelling is critically important for the success of a project, and have therefore used it extensively throughout all aspects of our project. Modelling is a very useful technique for a variety of reasons. Firstly, modelling a system before carrying out experiments is a great way to avoid wasting time and reagents in the lab. This is very valuable during projects that are time-constricted, such as the iGEM competition for example! Modelling a pathway before attempting to get experimental results also highlights any potential issues in the system, and helps target areas of interest within your chosen pathway. Any unusual results found after experimental work has been completed can sometimes be explained using modelling approaches.
We wanted to share our enthusiasm for modelling with the wider iGEM community, and feel there is currently no resource of teams to easily find out about the basics of modelling. At the YSB 1.0 conference, we discussed this with other teams and they agreed with us on this issue. Therefore we collaborated with the University of York and the University of Newcastle to produce tutorial videos on three different modelling softwares, explaining what each software is used for and the basics of how to use them.
The Registry of Standard Biological Parts already has a number of protocols for various standard wetwork methods. We hope that one day, a similar concept could be introduced to modelling.
In this video, the University of York team discuss the pros and cons of different types of modelling software that teams could potentially used for their model. This is followed by an introduction to the concept of delayed differential equations, and a guide showing how R can be used to to model them.
COPASI (COmplex PAthway SImulator) is open-source piece of software that can be used to model a wide range of biological systems, including metabolic networks and cell signalling pathways. In this video, the University Of Manchester team show you how to get started with COPASI by firstly creating a simple model of the first two reactions in the glycolysis pathway, followed by how to analyse something more complex
BioNetGen is often applied on rule-based modelling of biochemical networks utilizing the RuleBender interface. This video by Newcastle University team provides a brief tutorial on how to build a basic model on a reaction between a substrate and enzyme.
