Andrew Phillips
SCIENTIST
.
Programming Biology
We are currently developing visual programming languages and tools for simulating and analysing complex models of biological systems. One of our aims is to develop a language in which large models of biological systems can be programmed from simple components in a modular fashion. An ultimate goal is to be able to program and simulate a biological system on a computer, before implementing the final design inside a living organism.
Projects
- Stochastc Pi Machine (SPiM). A visual programming language for designing and simulating computer models of biological processes.
- Genetic Engineering of Cells (GEC). A programming language for genetic engineering of living cells.
- DNA Strand Displacement (DSD). A programming language for composable DNA circuits.
- Immune System Modelling. A quantitative model of MHC class I peptide editing.
- Gene Network Modelling. Compositional stochastic modelling of gene networks.
- Channel Ambient Machine (CAM). A distributed programming environment for developing mobile applications based on a formal model.
Press
- Science Fair for Grown Ups: Virtual Cells 4 March 2008
- Making Computer Systems Reveal Biological Secrets 8 March 2007
Bibtex
Publications: Journals
- Andrew Phillips and Luca Cardelli, A programming language for composable DNA circuits, in Journal of the Royal Society Interface, 17 June 2009
- Michael Pedersen and Andrew Phillips, Towards programming languages for genetic engineering of living cells, in Journal of the Royal Society Interface, 15 April 2009
- Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, and Andrew Phillips, A Process Model of Rho GTP-binding Proteins, in Theoretical Computer Science, Elsevier , 18 May 2009
- Andrew Phillips, An Abstract Machine for the Stochastic Bioambient Calculus, in Electronic Notes in Theoretical Computer Science, vol. 227, pp. 143-159, Elsevier , January 2009
- Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanogullari, and Andrew Phillips, A Process Model of Actin Polymerisation, in Electronic Notes in Theoretical Computer Science, vol. 229, no. 1, pp. 127-144, Elsevier , February 2009
- Ralf Blossey, Luca Cardelli, and Andrew Phillips, Compositionality, Stochasticity and Cooperativity in Dynamic Models of Gene Regulation, in HFSP Journal, vol. 2, no. 1, pp. 17–28, HFSP Publishing, February 2008
- Johannes Borgstroem, Andrew Gordon, and Andrew Phillips, A Chart Semantics for the Pi-calculus, in Electronic Notes in Theoretical Computer Science, vol. 194, no. 2, pp. 3–29, Elsevier, January 2008
- Andrew Phillips, Luca Cardelli, and Giuseppe Castagna, A Graphical Representation for Biological Processes in the Stochastic Pi-calculus, in Transactions in Computational Systems Biology, vol. 4230, pp. 123–152, Springer, November 2006
- Ralf Blossey, Luca Cardelli, and Andrew Phillips, A Compositional Approach to the Stochastic Dynamics of Gene Networks, in Transactions in Computational Systems Biology, vol. 3939, no. 3939, pp. 99–122, Springer, January 2006
Publications: Conferences
- Vinod Mugathan, Andrew Phillips, and Maria Vigliotti, BAM: BioAmbient Machine, in Application of Concurrency to System Design, IEEE Computer Society, September 2008
- Andrew Phillips and Luca Cardelli, Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus, in Computational Methods in Systems Biology, Springer, September 2007
- Andrew Phillips and Luca Cardelli, A Graphical Representation for the Stochastic Pi-calculus, in Concurrent Models in Molecular Biology, August 2005
- Andrew Phillips and Luca Cardelli, A Correct Abstract Machine for the Stochastic Pi-calculus, in Concurrent Models in Molecular Biology, August 2004
- Andrew Phillips, Nobuko Yoshida, and Susan Eisenbach, A Distributed Abstract Machine for Boxed Ambient Calculi, in European Symposium on Programming, Springer, April 2004
Publications: Books
- Andrew Phillips, A Visual Process Calculus for Biology, in Symbolic Systems Biology: Theory and Methods, Jones and Bartlett Publishers, In Press, 2009
- Andrew Phillips, Specifying and Implementing Secure Mobile Applications, in Process Algebra for Parallel and Distributed Processing , Chapman & Hall/CRC, December 2008
- Editors, Stephen Emmott, Ehud Shapiro, Stuart Rison, Andrew Phillips, and Andrew Herbert, Towards 2020 Science, Microsoft, March 2006
- Andrew Phillips, Specifying and Implementing Secure Mobile Applications in the Channel Ambient System, Ph.D. Thesis, April 2006
