Vincent Danos

Vincent Danos

Professor, Directeur de Recherches at CNRS

Departement d'Informatique, École Normale Supérieure de Paris, France

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)

I was:

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.

Interests

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).

Research projects I am involved in:

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

Former PhD students (since 2010):

  • John Wilson-Kanamori
  • Ricardo Honorato-Zimmer
  • Milana Filatenkova
  • Guoli Yang
  • Matthias Sachs (with Ben Leimkuhler, School of Mathematics)
  • Andreea Beica (ENS)
  • William Waites (Edinburgh)

Current PhD students:

  • Guillaume Terradot (Edinburgh, School of Biological Sciences, co-supervision)
  • Brian Coyle (Edinburgh, School of Computer Science, co-supervision)

About Kappa

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.