Russ Harmer גם זה יעבור

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).
Journées Nationales 2018 du réseau NETBIO (invited speaker). W3C Workshop on Web Standardization for Graph Data (invited participant).
Dagstuhl seminar on Big Graph Processing Systems (invited participant).

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).
ENS Lyon M2IF CR08 (Graph-based knowledge representation), 2019/20-2020/21 (M2). With Angela Bonifati.

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.

publications

#GDB = graph DBs, #KR = knowledge representation, #GR = graph rewriting, #RBM = rule-based modelling, #GS = game semantics
Knowledge representation and update in hierarchies of graphs. #GDB #KR #GR Russ Harmer and Eugenia Oshurko (2019). Submitted.
Bio-curation for cellular signalling: the KAMI project. #KR #GR #RBM Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré and Eugenia Oshurko. TCBB (to appear, 2019).
Schema validation and evolution for graph databases. #GDB #KR #GR Angela Bonifati, Peter Furniss, Alastair Green, Russ Harmer, Eugenia Oshurko and Hannes Voigt. arXiv. Submitted.
Bio-curation for cellular signalling: the KAMI project (extended abstract). #KR #GR #RBM Russ Harmer, Yves-Stan Le Cornec, Sébastien Légaré and Ievgeniia Oshurko. CMSB'17 (2017).
Rule-based meta-modelling for bio-curation. #KR #GR #RBM #GS Russ Harmer. Habilitation à Diriger des Recherches. ENS Lyon (2017). Soutenance.
A knowledge representation meta-model for rule-based modelling of cellular signalling. #KR #RBM Adrien Basso-Blandin, Walter Fontana and Russ Harmer. DCM'15 (2015). EPTCS 204, pp. 47-59 (2016).
Thermodynamic graph rewriting. #GR #RBM Vincent Danos, Russ Harmer and Ricardo Honorato-Zimmer. LMCS 11(2:13), pp. 1-26 (2015).
Deriving rate equations for site graph rewriting systems. #RBM Vincent Danos, Russ Harmer, Ricardo Honorato-Zimmer and Sandro Stucki. SASB'13.
Thermodynamic graph rewriting (extended abstract). #GR #RBM Vincent Danos, Russ Harmer and Ricardo Honorato-Zimmer. CONCUR'13.
Constraining rule-based dynamics with types. #GR #RBM Vincent Danos, Russ Harmer and Glynn Winskel. MSCS 23(2), pp. 272-289 (2013).
Graphs, rewriting and pathway reconstruction for rule-based models. #GR #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer, Jonathan Hayman, Jean Krivine, Chris Thompson-Walsh and Glynn Winskel. FSTTCS'12 (2012).
Models of the Tet-on system with epigenetic effects. #RBM Russ Harmer, Jean Krivine, Élise Laruelle, Cédric Lhoussaine, Guillaume Madelaine and Mirabelle Nebut. CMSB'12 (2012).
Intrinsic information carriers in combinatorial dynamical systems. #GR #RBM Russ Harmer, Vincent Danos, Jérôme Feret, Jean Krivine and Walter Fontana. Chaos 20(3), 037108 (2010).
Abstracting the differential semantics of rule-based models: exact and automated model reduction. #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. LICS'10 (2010).
Totality in arena games. #GS Pierre Clairambault and Russ Harmer. [pre-print] APAL 161(5):673--689 (2010).
Rule-based modelling and tunable resolution. #RBM Russ Harmer. DCM'09. EPTCS 9, pp. 65-72 (2009).
Rule-based modelling and model perturbation. #RBM 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 model refinement. #RBM Elaine Murphy, Vincent Danos, Jérome Feret, Russ Harmer and Jean Krivine. Chapter 4 of Elements of Computational Systems Biology (2009).
Internal coarse-graining of molecular systems. #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. PNAS 106(16):6453-6458 (2009).
Investigation of a biological repair scheme. #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. WMC'08 (2009).
Rule-based modelling, symmetries, refinement. #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. FMSB'08 (2008).
Rule-based modelling of cellular signalling. #RBM Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer and Jean Krivine. CONCUR'07 (2007).
Categorical combinatorics for innocent strategies. #GS Russ Harmer, Martin Hyland and Paul-André Melliès. LICS'07 (2007).
The anatomy of innocence revisited. #GS Russ Harmer and Olivier Laurent. FSTTCS'06 (2006).
An analysis of innocent interaction. #GS Russ Harmer. GaLoP 2, 2006.
Affine strategies in arena games. #GS Russ Harmer. GaLoP 1, 2005.
Probabilistic game semantics. #GS Vincent Danos and Russ Harmer. Special issue for LICS'00. ACM Transactions on Computational Logic 3(3) (2002).
The anatomy of innocence. #GS Vincent Danos and Russ Harmer. CSL'01 (2001).
Probabilistic game semantics (extended abstract). #GS Vincent Danos and Russ Harmer. LICS'00 (2000).
A fully abstract game semantics for finite nondeterminism. #GS Russ Harmer and Guy McCusker. LICS'99 (1999). PhD: tesi (vo, 31 decembre 1999) #GS

27.01.2019