RESEARCH PROFILE

My research in Computational Biology focuses on:

• Development of simulation techniques to model interaction between micro-organisms, in particular the use of cellular automata;
• Development of logic-based domain-specific languages to model bio-networks, such as metabolic pathways and signalling networks

In the area of Formal methods, I am particularly interested in:

• Development of verified optimizing compilers; I have been working towards an approach to specifying optimisations based on Temporal Logics, which allows for many interesting optimisations to be written out formally and proved;
• Race conditions and their implications in the correct execution of concurrent programs and distributed applications.

EDUCATION PROFILE

Courses Taught

• Computational Biology [details]
  A Masters-level module designed to introduce students to the application of computational techniques to solve biological problems. I will be covering metabolic pathways, simulation techniques, and protein structure.
• Compiler Design [details]
  The module provides a through introduction to the principles of compiler design, with an emphasis on general solutions to common problems as well as techniques for putting the extensive theory into practice.
• Undergraduate Project Supervision
  I have supervised dozens of students on successful projects, most of them being designed by the students themselves. Examples include pervasive computing, flight simulation, biochemical modelling, astrophysics, web-based tools.
• Software Lifecycle Management [details]
  The module aims to provide students with an in-depth understanding of issues affecting the deployment of large and complex computing systems in organisational settings. This module is taught in collaboration with IBM UK.
• Principles of Concurrency [details]
  This module provides students with an initial exposure to concepts such as message-passing, deadlock, and interleaving. A basic introduction to formal specification using CCS or CSP (two well-known process algebras) will provide students with a notation for discussing aspects of computation in a distributed environment.

CURRENT RESEARCH PROJECTS

• Verification of the Optimisation Phase of a Compiler, .., Project Start Date: 01/07/2006 Project End Date: 30/06/2010

SELECTED PUBLICATIONS

• Antony B Holmes, Sara Kalvala, David E Whitworth (2010) 'Spatial Simulations of Myxobacterial Development' PLoS Computational Biology 6 (2), (1553-734X) [article]
• Sara Kalvala, Richard Warburton, David Lacey (2009) 'Program transformations using temporal logic side conditions' ACM Transactions On Programming Languages And Systems 31 (4), (0164-0925) [article]
• Dominic Orchard, Jonathan Gover, Lee Lewis Herrington, James Lohr, Duncan Stead, Cathy Young, and Sara Kalvala (2009) 'muCell - Interdisciplinary Research in Modelling and Spatial Simulation of Multi-cellular Environments"' in Reinvention: A Journal of Undergraduate Research,
• Anthony Holmes, Sara Kalvala and David Whitworth (2009) 'Myxobacteria motility: a novel 3D model of rippling behaviour in Myxococcus xanthus' in Communications of the Systemics and Informatics World Network (CoSIWN), (1757-4439)
• Richard Warburton and Sara Kalvala (2009) 'From Specification to Optimisation: An Architecture for Optimisation of Java Bytecode' in Compiler Construction ,18th International Conference,, Editors: de Moor, Oege; Schwartzbach, Michael (978-3-642-00721-7), Springer Verlag

RECENT RESEARCH DEGREES SUPERVISED

• Understanding morphogenesis in myxobacteria from a theoretical and experimental perspective Date of Completion: 2009
• Formally specifying optimizations using TRANS Date of Completion: 2009
• Formalisation of Message Sequence Charts Date of Completion: 2009