Vincent Danos Edinburgh homepage

Vincent Danos - Edinburgh homepage

I am Directeur de Recherches at CNRS, Chair of Computational Systems Biology at the University of Edinburgh (under the SICSA funding scheme). I was Director of Synthsys the Centre for Synthetic and Systems Biology at Edinburgh in 2012-2013; an external faculty member of the Santa Fe Institute (2007-2009), and a visiting Professor at the Harvard Medical School (2006-2009).

I work on clean and scaleable domain-specific modeling/programming languages, mostly, but not only, for systems and synthetic biology. I am taking part in cross-disciplinary activities meeting on algorithmic/mathematical structures for modelling (social systems, economical systems, climate, multi-scale plant growth, etc) with the Edinburgh Multidisciplinary Multiscale Modelling initiative.

My current research projects include the following:
2014-2018: Big Mechanism programme (DARPA): Executable Knowledge (consultant).
2013-2018: ERC Advanced Fellowship (FP7): Rule-based modelling
2012-2015: EPSRC Flowers Consortium: Platform for Synthetic Biology

About Kappa

The Kappa modelling approach, which I co-invented, 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 incorpororated Kappa in a list of only three target formalisms (together with the standard SBML and SRI's Pathway Logic).

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 languages has various open-source implementations

Various academic activities since 2002 (Keynotes, invitations, courses, PCs).

Current PhD students:

- John Wilson-Kanamori
- Ricardo Honorato-Zimmer
- Milana Filatenkova
- Guoli Yang
- Matthias Sachs (with Ben Leimkuhler, School of Mathematics)