Formal software architecture for agent-based modelling in biology
The growing area of systems biology has been using agent-based models for many years with early models centred around the organism level. As we delve deeper into the mechanisms of organs and cells the number and complexity of agents will increase as models become more complex. Models of the differen...
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| Format | Dissertation |
| Language | English |
| Published |
University of Sheffield
2007
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| Online Access | Get more information |
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| Summary: | The growing area of systems biology has been using agent-based models for many years with early models centred around the organism level. As we delve deeper into the mechanisms of organs and cells the number and complexity of agents will increase as models become more complex. Models of the different types of biological cells in tissue growth (with their associated cell cycles, bonding, and signalling pathways) and the proteins and receptors in cell signalling pathways are being produced. With the increasing availability of supercomputer clusters and multi-core desktop machines to researchers these models can be run quickly and efficiently. The aim of this thesis is to facilitate the simulation of sufficiently formalised massively multi-agent simulations. This has been achieved by using techniques from software testing and utilising the message passing libraries of high performance computers. A number of case studies demonstrate the application of the approach for modelling different biological cell models, cell signalling pathways, and macro economics. |
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