Russ Harmer

russ harmer

russell point harmer arobase ens tiret lyon point fr Chargé de Recherche au CNRS Équipe PLUME (LIP, CNRS & ENS Lyon) Bureau GN1 Sud 355, 46 allée d'Italie, 69364 LYON Cedex 07

événements / events

GaLoP 1 workshop (PC member). ASCB annual meeting 2007, SIG 'Systems Biology of Receptor Tyrosine Kinase Networks' (invited speaker). GaLoP 3 workshop (co-chair). 1st International Workshop on Computational models for cell processes (invited speaker). Special issue of APAL for the GaLoP 3 workshop (co-editor). Biopathways 10 (invited speaker). 2nd International Workshop on Computational models for cell processes (PC member). 1st International Workshop on Interactions between Computer Science and Biology (PC member). 3rd LICS Workshop on Logic and Systems Biology (co-chair). 6th International Workshop on Developments in Computational Models (invited speaker). 3rd International Workshop on Computational models for cell processes (PC member). Workshop on Systems Biology and Formal Methods (invited speaker). 4th LICS Workshop on Logic and Systems Biology (co-chair). 3rd SASB International Workshop (invited speaker). Rule Base in Paris (co-organizer). 4th SASB International Workshop (PC member). 4th International Workshop on Computational models for cell processes (PC member). 5th International Workshop on Interactions between Computer Science and Biology (PC member). 5th LICS workshop on Logic and Systems Biology (co-chair). 10th International Workshop on Developments in Computational Models (co-chair). Trends in graph transformation (co-organizer). Special issue of EPTCS for the DCM 2014 workshop (co-editor).
11th International Workshop on Developments in Computational Models (PC member). 1st LIP seminar on Languages, Semantics and Compilation (invited speaker). 8th Workshop on Information and Processes (invited speaker). 2nd LIP seminar on Languages, Semantics and Compilation (co-organizer). 6th LICS workshop on Logic and Systems Biology (co-chair).
3rd LIP seminar on Languages, Semantics and Compilation (co-organizer). 3rd LyonSysBio Meet the Industry (invited speaker).

enseignement / teaching

MPRI 2-02 (Modèles des langages de programmation: domaines, catégories, jeux), 2004/05-2007/08 (M2). [lecture notes] MPRI 2-19 (Méthodes informatiques pour la biologie systémique et synthétique), 2008/09 (M2). AIV CompBio 2 (Rule-based modeling), 2011/12-2013/14 (M1). ENS Lyon M2IF CR02 (Linear logic & game semantics), 2013/14 (M2).
ENS Lyon M2IF CR11 (Rule-based modelling), 2014/15-2015/16 (M2). Groupe de lecture / reading group (théorie des catégories / category theory), 2015/16 (L3/M1).

projets / projects

Executable Knowledge (DARPA Big Mechanism). Active Context (DARPA CwC bio-curation use case).

modélisation à base de règles / rule-based modeling

Rule-based modelling of cellular signalling. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. CONCUR'07 (2007).
Rule-based modelling, symmetries, refinement. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. FMSB'08 (2008).
Investigation of a biological repair scheme. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. WMC'08 (2009).
Internal coarse-graining of molecular systems. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. PNAS 106(16):6453-6458 (2009).
Rule-based modelling and model refinement. Elaine Murphy, Vincent Danos, Jérome Feret, Russ Harmer and Jean Krivine. Chapter 4 of Elements of Computational Systems Biology (2009).
Rule-based modelling and model perturbation. [pre-print] Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. Transactions on Computational Systems Biology XI, pp. 116-137 (2009).
Rule-based modelling and tunable resolution. Russ Harmer. DCM'09. EPTCS 9, pp. 65-72 (2009).
Abstracting the differential semantics of rule-based models: exact and automated model reduction. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. LICS'10 (2010).
Intrinsic information carriers in combinatorial dynamical systems. [pre-print] Russ Harmer, Vincent Danos, Jérôme Feret, Jean Krivine and Walter Fontana. Chaos 20(3), 037108 (2010).
Models of the Tet-on system with epigenetic effects. Russ Harmer, Jean Krivine, Élise Laruelle, Cédric Lhoussaine, Guillaume Madelaine and Mirabelle Nebut. CMSB'12 (2012).
Graphs, rewriting and pathway reconstruction for rule-based models. Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh and Glynn Winskel. FSTTCS'12 (2012).
Constraining rule-based dynamics with types. [pre-print] Vincent Danos, Russ Harmer and Glynn Winskel. MSCS 23(2), pp. 272-289 (2013).
Thermodynamic graph rewriting (extended abstract). Vincent Danos, Russ Harmer and Ricardo Honorato-Zimmer. CONCUR'13.
Deriving rate equations for site graph rewriting systems. Vincent Danos, Russ Harmer, Ricardo Honorato-Zimmer and Sandro Stucki. SASB'13.
Thermodynamic graph rewriting. Vincent Danos, Russ Harmer and Ricardo Honorato-Zimmer. LMCS 11(2:13), pp. 1-26 (2015).
A knowledge representation meta-model for rule-based modelling of cellular signalling. Adrien Basso-Blandin, Walter Fontana and Russ Harmer. DCM'15 (2015). EPTCS 204, pp. 47-59 (2016).

sémantique de jeux / game semantics

A fully abstract game semantics for finite nondeterminism. Russ Harmer and Guy McCusker. LICS'99 (1999). PhD: tesi (vo, 31 decembre 1999)
Probabilistic game semantics (extended abstract). Vincent Danos and Russ Harmer. LICS'00 (2000).
The anatomy of innocence. Vincent Danos and Russ Harmer. CSL'01 (2001).
Probabilistic game semantics. Vincent Danos and Russ Harmer. Special issue for LICS'00. ACM Transactions on Computational Logic 3(3) (2002).
Affine strategies in arena games. Russ Harmer. GaLoP 1, 2005.
An analysis of innocent interaction. Russ Harmer. GaLoP 2, 2006.
The anatomy of innocence revisited. Russ Harmer and Olivier Laurent. FSTTCS'06 (2006).
Categorical combinatorics for innocent strategies. Russ Harmer, Martin Hyland and Paul-André Melliès. LICS'07 (2007).
Totality in arena games. Pierre Clairambault and Russ Harmer. [pre-print] APAL 161(5):673--689 (2010).

11.03.2016