IGEM:IMPERIAL/Methodology/Modelling

• Overview
• Specifications
• Design
• Modelling
• Implementation
• Testing/Validation

Description

Once the Design documents have been delivered, the modelling stage will bring a more qualitative and quantitative analysis to the problem. A clear physical interpretation of the system followed by an adequate mathematical description is needed to shed insight into its behaviour. The ability to predict system behaviour with a model helps evaluate model completeness as well as improve our understanding of the mechanisms of biological processes. The model should have the same interface (Inputs/Outputs) as the ones specified. Specified transfer functions and performances can be predicted.

Deliverables

• define inputs and outputs.
• list all the variables and parameters of the model in a table, specifying if their values are known, unknown, to be measured.
• comment on the different assumptions you have made when modelling.
• comment on the sensitivity of key parameters.
• image of the model.
• a file describing the model in a standardized format (SBML, CellML).
• predicted transfer functions.

Tools

• A huge number of tools are available to deal with biological modelling. We would recommend to use the ones based on standardized description languages such as SBML, CellML (to promote collaborations and exchange of data). We used SBML based CellDesigner as it provides a nice GUI to edit models.
• Some more advance modelling was also done in Matlab (but it might create a gap amongst students as some of them have never used a programming language).