Directeur de Recherches at CNRS, at the Departement d’Informatique of ENS (DI-ENS, UMR 8548), at Team Antique
Chair of Computational Systems Biology at the School of Informatics, at the University of Edinburgh (on leave of absence)
Director of Synthsys the Centre for Synthetic and Systems Biology at Edinburgh (2012-2013);
external faculty member of the Santa Fe Institute (2007-2009); and
visiting Professor at the Harvard Medical School (2006-2009) at the Fontana lab.
I work on clean and scaleable domain-specific modeling/programming languages, mostly, but not only, for systems and synthetic biology. I have a research interest in cross-disciplinary activities and convergence on algorithmic/mathematical structures for modelling (social systems, economical systems, climate, multi-scale plant growth, etc).
Academic Activities (Keynotes, invitations, courses, PCs, since 2002).
2015-2019: SBRC centre for mammalian synthetic biology at SynthSys
2014-2018: Big Mechanism programme (DARPA): Executable Knowledge (consultant).
2013-2018: ERC Advanced Fellowship RULE on Rule-based modelling
2012-2017: EPSRC Flowers Consortium: Platform for Synthetic Biology
2016-2019: ANR REPAS
The Kappa modelling approach, which I co-invented (with Cosimo Laneve), was featured twice in Nature in 2009, and hailed as one of the future “mainstream components of modern quantitative biology” in a 2011 paper in Nature Methods. The Edinburgh entry to the prestigious international iGEM synthetic biology competition used Kappa as a modelling language and was twice awarded the Best Model Prize (2010, 2011). The 2014-2018 DARPA “Big Mechanism” programme on cancer biology has incorporated Kappa in a list of only three target formalisms (together with the standard SBML and SRI’s Pathway Logic). It forms part of the material of a series of lectures at College de France by Walter Fontana, Fall 2019.
Here is 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 language has an open-source implementation currently under active development.