University of Edinburgh, United Kingdom

Description of organizationuniversity of edinburgh

The School of Informatics at the University of Edinburgh is widely recognized as one of the strongest groupings of researchers working in informatics worldwide. The school is organized in several research institutes including the Laboratory for Foundations of Computer Science (LFCS) and Institute for Artificial and Neural Computation (IANC). Within the LFCS there is considerable expertise in formal modeling techniques for biological systems, relating formal modeling languages to sophisticated mathematical interpretations and software development to support them.

 

The University also hosts the Centre for Systems Biology at Edinburgh (CSBE, now SynthSys), one of six Centres for Integrative Systems Biology funded by the UK government through the Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC).

 

Previous experience

Professor Jane Hillston is the Director of the Laboratory for Foundations of Computer Science and one of the Principal Investigators of CSBE/SynthSys. She has participated in several EU projects (IMSE, DEGAS and SENSORIA) and received substantial funding from the EPSRC to support her work on formal modeling languages for dynamic modeling in systems biology and performance evaluation, including a prestigious Advanced Research Fellowship.

 

Professor Stephen Gilmore is the Chair of Software Systems Modeling and another of the Principal Investigators of CSBE/SynthSys. He has been involved in a number of EU-funded projects (Fireworks, MRG, DEGAS, and SENSORIA) and has received funding from the EPSRC and the BBSRC.

 

Dr Guido Sanguinetti is a member of Institute of Artificial and Neural Computation and a member of the management board of SynthSys. Dr Sanguinetti has held funding from BBSRC, EPSRC, Microsoft Research, EMBO and the EU.

 

Profile of staff members

Jane Hillston is a world leader in the design of quantified modeling languages and associated analysis techniques. She has been working the area of systems biology for the last ten years.

Stephen Gilmore's research is focused on the provision of high-level software tools for efficient computational modeling and parameter estimation on high-performance parallel computing platforms.

Guido Sanguinetti's research focuses on machine learning methods for dynamical modelling in biology. He has developed novel inference techniques for continuous time models in Systems Biology.

 

Webpage

School of Informatics at the University of Edinburgh

 

 

Five recent publications relevant to the project

1) Bio-PEPA: A Framework for the Modelling and Analysis of Biological Systems, F. Ciocchetta and J. Hillston, in Theoretical Computer Science 410 (33-34), pp. 3065-3084, 2009. http://dx.doi.org/10.1016/j.tcs.2009.02.037

 

2) Formal Methods for Checking the Consistency of Biological Models, A. Clark, V. Galpin,

S. Gilmore, M-L. Guerriero and J. Hillston, in ''ICSB 2010 Proceedings: Advances in Systems Biology", Springer-Verlag, December 2011.

 

3) On verifying Bio-PEPA models, Allan Clark, Stephen Gilmore, Maria Luisa Guerriero and Peter Kemper, 8th International Conference on Computational Methods in Systems Biology (CMSB 2010), Trento, Italy, pages 23-32, October 2010.

 

4) Andrea Ocone and Guido Sanguinetti, Reconstructing transcription factor activities in hierarchical transcription network motifs, Bioinformatics 27(20):2873-9 (2011).

 

5) G. Sanguinetti, J. Noirel and P.C. Wright, MMG: a probabilistic tool to identify submodules of metabolic pathways, Bioinformatics 24(8), 1078-1084 (2008).