SPA Conference session: Software for Programming Cells

One-line description:Compiling descriptions of biological behaviour to DNA code
Session format: Lecture + tutorial [read about the different session types]
Abstract:Cells are the building blocks of all life. If we could program living cells as effectively as we program digital computers, we could make fundamental breakthroughs in the treatment of disease, the development of sustainable agriculture and the production of clean energy, while also gaining insight into the workings of life itself. In spite of this promise there are still many challenges to overcome. First and foremost, programming cells remains highly complex and error-prone, and we have reached a point where powerful computer software is needed to accelerate further progress. This session presents computer software for programming cells at three levels: molecular circuits, genetic devices and cell colonies. We present a molecular program of an optimal consensus algorithm and show results of the working system implemented in DNA. We also present a software tool chain for characterising genetic parts that can be combined into genetic devices for programming cell function. Finally, we present software that, for the first time, simulates cell biofilms using 3D biophysical methods, and predicts the effect of cell shape on colony morphology. Just as software for programming digital computers heralded a new era of technology, software for programming cells could enable new industries in biotechnology.
Audience background:Interest in biology and in programming languages. No prior knowledge of either is required.
Benefits of participating:Learning about the role of software for biotechnology and for computational modelling of biological processes.
Materials provided:Online demos, online documentation, pdf attachments.
Process:An overview of the field, demonstrations of the software, and a couple of exercises to try out online
Detailed timetable:00:00 Introduction to how software could play a key role in Biotechnology
00:15 Demos of examples
00:35 Interactive session
01:00 Conclusion
Outputs:Slides, key references as pdf attachments, online documentation, online tools that run in a browser.
History:Some of the material presented as a tutorial for the Cambridge iGEM (international Genetically Engineered Machines) competition. Material also presented as a tutorial at the DNA17 international conference on DNA computing and Molecular programming 2011.
1. Andrew Phillips
Microsoft Research
2. Colin Gravill
Microsoft Research