Russ Harmer

russ harmer

russell point harmer arobase ens tiret lyon point fr Chargé de Recherche au CNRS Chef de l'équipe PLUME (LIP, CNRS - ENS Lyon - UCBL1 - Université de Lyon) Bureau GN1 Nord 326, 46 allée d'Italie, 69364 LYON Cedex 07

séminaires / seminars

Le groupe de travail de l'équipe Plume. Séminaire LSC (Langages, Sémantique, Compilation) du LIP (co-organizer and steering committee). Séminaire mensuel CHoCoLa.

événements / events

arXiv 5th International Workshop on Interactions between Computer Science and Biology (PC member). 5th CSL-LICS-VSL 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 International Workshop on Information and Processes (invited speaker). 6th LICS Workshop on Logic and Systems Biology (co-chair and speaker). 3rd LyonSysBio Conference: Meet the Industry (invited speaker).
15th International Conference on Computational Methods for Systems Biology (invited speaker). Journées Nationales 2018 du GDR Informatique Mathématique (invited speaker).
12th International Workshop on Developments in Computational Models (PC member). 7th LICS-FLOC Workshop on Logic and Systems Biology (co-chair). 27th International Conference on Computer Science Logic (PC member). Workshop on Discrete models and formal verification in biology (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). BioQurate (FIL projet transversal).

développement logiciel / software development

KAMI: Knowledge Aggregator and Model Instantiator. ReGraph: graph rewriting library in Python. More detail on the overall Kappa project.

bio-curation

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).
Rule-based meta-modelling for bio-curation. Russ Harmer. Habilitation à Diriger des Recherches. ENS Lyon (2017). Soutenance.
Bio-curation for cellular signalling: the KAMI project (extended abstract). [pre-print] Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré and Ievgeniia Oshurko. CMSB'17 (2017).

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).

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).

27.11.2017