Contact information
- pierre.boutillier_AT_ens-lyon.org
- https://github.com/pirbo
- https://gitlab.com/pirbo
Kappa softwares
Kappa is a domain specific language designed to model protein-protein interaction based on stochastic graph rewrites. I work on 3 axes:
- Algorithmic&compilation: Efficiency of the interpreter (the simulator)
- Software ingineering: Interactibility with biologist (User interface and exposure as a python library)
- Porgraming language for graph inspection (the mixture of proteins)
- Pierre Boutillier: The Kappa Simulator Made Interactive. CMSB 2019
- Pierre Boutillier, Ioana Cristescu, Jérôme Feret: Counters in Kappa: Semantics, Simulation, and Static Analysis. ESOP 2019
- Pierre Boutillier, Mutaamba Maasha, Xing Li, Héctor F. Medina-Abarca, Jean Krivine, Jérôme Feret, Ioana Cristescu, Angus G. Forbes, Walter Fontana: The Kappa platform for rule-based modeling. Bioinformatics 34(13)
- Angus Graeme Forbes, Andrew Burks, Kristine Lee, Xing Li, Pierre Boutillier, Jean Krivine, Walter Fontana: Dynamic Influence Networks for Rule-Based Models. IEEE Trans. Vis. Comput. Graph. 24(1)
- Jonathan Laurent, Héctor F. Medina-Abarca, Pierre Boutillier, Jean Yang, Walter Fontana: A Trace Query Language for Rule-Based Models. CMSB 2018
- Pierre Boutillier, Ferdinanda Camporesi, Jean Coquet, Jérôme Feret, Kim Quyên Lý, Nathalie Théret, Pierre Vignet: KaSa: A Static Analyzer for Kappa. CMSB 2018
- Pierre Boutillier, Thomas Ehrhard, Jean Krivine: Incremental Update for Graph Rewriting. ESOP 2017
OCaml expertise
The tezos blockchain code base is in OCaml and Nomadic Labs works on its development with strong concern for formal methods. I'm involved in the release process there.
I take any occasion to write programs in my mother tongue and freelanced to do so on several other occasion.
Inductive in Coq
I was PhD student in Université Paris Diderot in PPS lab suppervised by Hugo Herbelin about dependently typed programming inside the Coq proof assistant.
I've kept as archeology the webpage (in French) about my defense.
During my PhD, I spent nearly all my time, hacking Coq.
Training in theoretical computer science
I have been student at the École normale supérieure de Lyon in the Computer Science Department for two years. Then, I studied at the MPRI. My interships dealt about:
- 2008
- Terminaison en PI-Calcul (PLUME @ LIP ENS Lyon) under the responsibility of Romain Demangeon and Sebastien Briais.
- 2009
- Equality over lambda-terms with list primitives (MSP @ Computer and Informations Sciences departement Strathclyde university) under the supervision of Conor McBride.
- 2010
- Dependent pattern-matching in Coq (Πr2 @ INRIA Rocquencourt) with Hugo Herbelin.
- Guillaume Allais, Conor McBride, Pierre Boutillier: New equations for neutral terms: a sound and complete decision procedure, formalized. DTP@ICFP 2013
Teaching material in French
- 2010/2011
- TD algorithmique M1 et TP initiation à la programmation L1
- 2011/2012 - 2012/2013
- TD d'initiation à l'algorithmique pour la licence de BioInfo et Cours/TP d'initialtion aux systèmes d'exploitation L1
- 2013
- TP programmation fonctionnelle L3, TP analyse lexicale et syntaxique L3 et TD Compilation M1
- 2015
- TP de Caml Light en MPSI
- 2020
- Computationnal biology Master