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 and multi-agent modelling;
• Development of logic-based domain-specific languages to model bio-networks, such as metabolic pathways and signalling networks, and synthetic analogues of biosystems.

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.

TEACHING PROFILE

Courses Taught

• Programming Language Design and Semantics [details]
  Covering type systems in modern programming languages, and the role of type disciplines in the design and evolution of programming languages.
• Programming for Computer Scientists [details]
  Java for First-Year students in Computer Science and related joint degrees.
• 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.

SELECTED PUBLICATIONS

• Sara Kalvala and Richard Warburton(2011) 'A Formal Approach to Fixing Bugs' in Formal Methods: Foundations and Applications, (978-3-642-25031-6), Springer-Verlag
• Holmes, A. B., Kalvala, S. and Whitworth, D. E.(2010) 'Spatial simulations of myxobacterial development' PLoS Computational Biology 6 (2), e1000686 (1553-734X) [article]
• Kalvala, S., Warburton, R. and Lacey, D.(2009) 'Program transformations using temporal logic side conditions' ACM Transactions On Programming Languages And Systems 31 (4), 14 (0164-0925) [article]
• Chien-An Chen, Sara Kalvala, Jane Sinclair(2005) 'A Process-Based Semantics for Message Sequence Charts with Data' in Australian Software Engineering Conference 2005 (Proceedings), (0-7695-2257-2), IEEE Computer Society
• Chien-An Chen, Sara Kalvala, Jane Sinclair(2005) 'Race Conditions in Message Sequence Charts' in APLAS 2005, LNCS 3780, (3-540-29735-9), Springer

RESEARCH DEGREES SUPERVISED

• On the Generation and Analysis of Program Transformations, Date of Completion: 2010
• 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