I am Directeur de Recherches at CNRS (Paris, PPS lab), Professor at the University of Edinburgh (under the SICSA funding scheme), and was until recently an external faculty member of the Santa Fe Institute, and a visiting Professor at the Harvard Medical School (Fontana lab).
I am interested in domain-specific modeling/programming languages, mostly, but not only, in the context of systems and synthetic biology. In the larger view my interest is towards formal approaches to complex systems, where syntax meets dynamics (and learning). I belong to the ILSI and LFCS labs. My methodology is based on mathematics.
Here is a Nov 2009 Nature feature article mentioning the kappa language which we have developed to model biomolecular networks. Here is another one (Jul 2009). Yet another one in a recent issue of Nature Methods (Feb 2011) - with a vibrant endorsement of our rule-based methods!
A short intro to rule-based modelling:
Agile modelling of cellular signalling
(SOS'08)
A longer one:
Rule-based modelling of cellular signalling (CONCUR'07)
Our modelling languages has various open-source implementations
Most of my publications can be found here (Paris homepage), there (google scholar), or there (DBLP).
A workshop on the fragility of networks held Dec 10 2010 at the Informatics Forum with J. Michael Herrmann and Matthias Hennig (UoE).
A wonderful and wonderfully amusing talk about the aims of education (pdf taken from the James Lynch homepage).
Interested in a PhD? Application information is here.
Interested in a UG project? Check this (internal UoE link).
M. Sc. Teaching:
- Synthetic biology and modeling
- Methods for the Analysis of Networks
Various academic activities since 2002 (Keynotes, invitations, courses, PCs).
PhD students:
- Elaine Murphy
- John Wilson-Kanamori
- Ricardo Honorato
- Donal Stewart