@misc{michel92,
author = {Michel, O.},
title = {Une plateforme logicielle pour l'expérimentation
d'algorithmes de simulation parallèle. Application à
{T}ime-{W}arp},
note = {Rapport de stage du DEA MISI de l'UPMC Paris VI},
institution = {Laboratoire de Recherche en Informatique, UMR 8623 du CNRS},
year = {1992},
month = sep,
kind = {rapport},
equipe = {specif},
url = {},
localurl = {}
}
@inproceedings{DBLP:conf/sas/GiavittoSM92,
author = {Giavitto, Jean-Louis and Sansonnet, Jean-Paul and Michel, Olivier},
title = {Inf{\'e}rer rapidement la g{\'e}om{\'e}trie des collections.},
booktitle = {WSA},
year = {1992},
pages = {185-193},
bibsource = {DBLP, http://dblp.uni-trier.de},
localurl = {~michel/PUBLIS/1992/PUBLIS/wsa92.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1992/wsa92.ps.gz}
}
@inproceedings{michel94c,
author = {Michel, O. and De Vito, D.},
title = {8,5 un environnement de développement pour le
langage 8{\scriptsize1/2}},
booktitle = {Journées du GDR Programmation},
address = {Lille, 22-23 Septembre 1994},
publisher = {GDR Programmation du CNRS},
year = {1994},
kind = {colloque},
equipe = {specif},
localurl = {~michel/PUBLIS/1994/PUBLIS/gdr94.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1994/gdr94.ps.gz}
}
@inproceedings{michel94b,
author = {Michel, O. and Giavitto, {J.-L.}},
title = {Design and Implementation of a Declarative
Data-parallel Language},
booktitle = {post-ICLP'94 workshop W6 on Parallel and Data
Parallel Execution of Logic Programs},
address = {S. Margherita Liguria, Italy},
publisher = {Uppsala University, Computing Science Department},
year = {1994},
month = jun,
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1994/PUBLIS/iclp.data-parallel.2.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1994/iclp.data-parallel.2.ps.gz}
}
@inproceedings{michel94,
author = {Michel, O. and Giavitto, J.-L. and Sansonnet, J.-P.},
title = {A data-parallel declarative language for the
simulation of large dynamical systems and its
compilation},
booktitle = {SMS-TPE'94: Software for Multiprocessors and
Supercomputers},
address = {Moscow, 21-23 September },
publisher = {Office of Naval Research USA \& Russian Basic
Research Foundation},
year = {1994},
pages = {103--111},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1994/PUBLIS/SMS-TPE-moscow.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1994/SMS-TPE-moscow.ps.gz}
}
@inproceedings{michel95c,
author = {Michel, O. and Giavitto, J.-L.},
title = {Typer une collection par la présentation d'un
groupe},
booktitle = {Journées du GDR Programmation},
address = {Grenoble, 23-24 Novembre 1995},
publisher = {GDR Programmation du CNRS},
year = {1995},
kind = {colloque},
equipe = {specif},
localurl = {~michel/PUBLIS/1995/PUBLIS/gdr95.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1995/gdr95.ps.gz}
}
@unpublished{michel95b,
author = {Michel, O.},
title = {The 8{\scriptsize1/2}\ reference manual},
note = {(personnal memo)},
institution = {Université de Paris-Sud, Orsay},
year = {1995},
number = {internal report of the 8{\scriptsize1/2}\ team},
month = dec,
url = {},
localurl = {},
kind = {rapport},
equipe = {specif}
}
@inproceedings{giavitto95,
author = {Giavitto, J.-L. and Michel, O. and Sansonnet, J.-P.},
title = {Group based fields},
editor = {Takayasu, I. and Halstead, R. H. Jr. and Queinnec,
C.},
volume = {1068},
series = {Lecture Notes in Computer Science},
pages = {209--215},
booktitle = {Parallel Symbolic Languages and Systems
(International Workshop PSLS'95)},
year = {1995},
publisher = {Springer Verlag},
address = {Beaune (France)},
month = {2--4 } # oct,
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1995/PUBLIS/psls.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/1995/psls.pdf}
}
@techreport{michel95a,
author = {Michel, O.},
title = {Design and implementation of 8{\scriptsize1/2}, a
declarative data-parallel language},
institution = {Laboratoire de Recherche en Informatique, UMR 8623 du CNRS},
year = {1995},
number = {1012},
month = dec,
kind = {rapport},
equipe = {specif},
localurl = {~michel/PUBLIS/1995/PUBLIS/rt-1012.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1995/rt-1012.ps.gz}
}
@article{michel96,
author = {Michel, O.},
title = {Design and implementation of 8{\scriptsize1/2}, a
declarative data-parallel language},
journal = {Computer Languages},
publisher = {Elsevier Science Publishers},
year = {1996},
volume = {22},
number = {2/3},
pages = {165--179},
note = {special issue on {P}arallel {L}ogic {P}rogramming},
kind = {intrevue},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/ComputerLanguages.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/ComputerLanguages.pdf}
}
@inproceedings{devito96a,
author = {De Vito, D. and Michel, O.},
title = {Effective {SIMD} code generation for the high-level
declarative data-parallel language 8{\scriptsize
1/2}},
booktitle = {EuroMicro'96},
year = {1996},
month = {2--5 } # sep,
adress = {Prague},
pages = {114--119},
publisher = {IEEE Computer Society},
kind = {intconf},
equipe = {specif},
localurl = {},
url = {}
}
@inproceedings{michel96b,
author = {Michel, O.},
title = {Introducing Dynamicity in the Data-Parallel Language
8{\scriptsize1/2}},
editor = {Luc Bougé and Pierre Fraigniaud and Anne Mignotte
and Yves Robert},
booktitle = {EuroPar'96 Parallel Processing},
volume = {1123},
pages = {678--686},
series = {Lecture Notes in Computer Science},
year = {1996},
month = aug,
adress = {Lyon (France)},
publisher = {Springer Verlag},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/w21.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/w21.pdf}
}
@inproceedings{michel96z,
author = {Olivier Michel},
title = {A Straightforward Translation of D0L Systems in the Declarative Data-Parallel Language 8{\scriptsize1/2}},
booktitle = {Euro-Par '96: Proceedings of the Second International Euro-Par Conference on Parallel Processing},
year = {1996},
isbn = {3-540-61626-8},
pages = {714--717},
publisher = {Springer-Verlag},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/w11.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/w11.ps.gz}
}
@inproceedings{michel96e,
author = {Michel, Olivier},
title = {Les amalgames : un mécanisme pour la structuration
et la construction incrémentielle de programmes déclaratifs},
booktitle = {Journées du GDR Programmation},
address = {Orléans},
publisher = {GDR Programmation du CNRS},
year = {1996},
month = {20--22 } # sep,
kind = {colloque},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/gdr96.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/gdr96.ps.gz}
}
@inproceedings{michel96a,
author = {Michel, O. and De Vito, D. and Sansonnet, J.-P.},
title = {8{\scriptsize1/2}\,: data-parallelism and data-flow},
booktitle = {{I}ntensional {P}rogramming {II}:Proc. of the 9th
Int. Symp. on {L}ucid and {I}ntensional
{P}rogramming},
editor = {Ashcroft, E.},
year = {1996},
publisher = {World Scientific},
month = may,
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/islip96.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/islip96.ps.gz}
}
@phdthesis{michel96d,
author = {Michel, O.},
title = {Représentations dynamiques de l'espace dans un
langage déclaratif de simulation},
school = {Université de Paris-Sud, centre d'Orsay},
year = {1996},
month = dec,
note = {N$^\circ 4596$, (in french)},
localurl = {~michel/PUBLIS/1996/PUBLIS/phd.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/phd.ps.gz}
}
@misc{giavitto96d,
author = {Sansonnet, J.-P. and Giavitto, J.-L. and Michel,
O. and Mahiout, A. and De Vito, D.},
title = {Rapport d'activité du thème 8{\scriptsize1/2} --
8{\scriptsize1/2} : Modèles et outils pour les
grandes simulations},
howpublished = {rapport interne (45p.)},
year = {1996},
month = jan,
kind = {rapport},
equipe = {specif},
localurl = {},
url = {}
}
@inproceedings{giavitto97a,
author = {Giavitto, J.-L. and De Vito, D. and Michel, O.},
title = {Semantics and Compilation of Recursive Sequential
Streams in 8{\footnotesize1/2}},
editor = {Glaser, H. and Kuchen, H.},
volume = {1292},
series = {Lecture Notes in Computer Science},
pages = {207--223},
booktitle = {Ninth International Symposium on Programming
Languages, Implementations, Logics, and Programs
(PLILP'97)},
year = {1997},
publisher = {Springer Verlag},
address = {Southampton},
month = {3--5 } # sep,
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1997/PUBLIS/plilp97.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/1997/plilp97.pdf}
}
@techreport{michel98,
author = {Olivier Michel and Jean-Louis Giavitto},
title = {Amalgams: Names and Name Capture in a Declarative
Framework},
institution = {LaMI -- Université d'Évry Val d'Essonne},
year = 1998,
number = {32},
month = jan,
note = {also avalaible as LRI Research-Report RR-1159},
localurl = {~michel/PUBLIS/1996/PUBLIS/rapport-amalgame.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/rapport-amalgame.ps.gz}
}
@inproceedings{giavitto99a,
author = {Giavitto, J.-L. and Michel, O.},
title = {Calcul distribué de champs de données},
booktitle = {Journées Francophones des Langages Applicatifs
(JFLA99)},
month = feb,
year = {1999},
address = {Avoriaz},
editor = {P. Weis},
publisher = {INRIA},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1999/PUBLIS/JFLA99.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1999/JFLA99.ps.gz}
}
@inproceedings{giavitto00a,
author = {Giavitto, J.-L. and Michel, O.},
title = { Un cadre pour la définition récursive de données},
booktitle = {Journées Francophones des Langages Applicatifs
(JFLA00)},
month = feb,
year = {2000},
address = {Mont Saint-Michel},
editor = {C. Dubois},
publisher = {INRIA},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/1996/PUBLIS/JFLA00.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/1996/JFLA00.ps.gz}
}
@inproceedings{giavitto01b,
author = {Jean-Louis Giavitto and Olivier Michel},
title = {MGS: a Rule-Based Programming Language for Complex
Objects and Collections},
booktitle = {Electronic Notes in Theoretical Computer Science},
volume = {59},
issue = {4},
publisher = {Elsevier Science Publishers},
editor = {Mark van den Brand and Rakesh Verma},
year = {2001},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2001/PUBLIS/entcs01.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2001/entcs01.pdf}
}
@inproceedings{giavitto01e,
author = {J.-L. Giavitto and O. Michel and F. Delaplace},
title = {Declarative simulation of dynamicals systems : the
{$8 1/2$} programming language and its application
to the simulation of genetic networks},
booktitle = {Proceedings of IPCAT 2001 (Workshop on Information
Processing in Cells and Tissues)},
month = aug,
year = {2001},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2001/PUBLIS/ipcat.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/2001/ipcat.ps.gz}
}
@inproceedings{giavitto01c,
author = {Jean-Louis Giavitto and Olivier Michel},
title = {Declarative definition of group indexed data structures and approximation of their domains},
booktitle = {PPDP '01: Proceedings of the 3rd ACM SIGPLAN international conference on Principles and practice of declarative programming},
year = {2001},
isbn = {1-58113-388-X},
pages = {150--161},
location = {Florence, Italy},
doi = {http://doi.acm.org/10.1145/773184.773201},
publisher = {ACM Press},
address = {New York, NY, USA},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2001/PUBLIS/ppdp01.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2001/ppdp01.pdf}
}
@manual{tutorielMGS,
title = {Une présentation du langage {MGS}},
author = {Giavitto, J.-L. and Michel, O. and Cohen, J.},
organization = {LaMI, universit\'e d'Evry},
month = may,
year = {2002},
note = {(tutoriel)},
kind = {rapport},
equipe = {specif},
localurl = {},
url = {}
}
@techreport{giavitto01R,
author = {Giavitto, J.-L. and Michel, O.},
title = {\texttt{MGS}: a Programming Language for the
Transformations of Topological Collections},
institution = {LaMI -- Universit{\'e} d'{\'E}vry Val d'Essonne},
year = 2001,
number = {61-2001},
month = may,
kind = {rapport},
equipe = {specif},
localurl = {~michel/PUBLIS/2001/PUBLIS/lami-RR61--mgs.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2001/lami-RR61--mgs.pdf}
}
@inproceedings{giavitto01d,
author = {J.-L. Giavitto and O. Michel},
title = {MGS: Implementing a Unified View on Four
Biologically Inspired Computational Models},
booktitle = {Pre-proceedings of WMC-CdeA 2001 (Workshop on
Membrane Computing, Curtea de Arges)},
month = aug,
publisher = {Research Report 17/01 of the Universitat Rivira I
Virgili, Tarragona, Spain},
year = {2001},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2001/PUBLIS/wmc01.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/2001/wmc01.ps.gz}
}
@article{norris02,
author = {Patrick Amar and Pascal Ballet and Georgia
Barlovatz-Meimon and Arndt Benecke and Gilles Bernot
and Yves Bouligand and Paul Bourguine and Franck
Delaplace and Jean-Marc Delosme and Maurice Demarty
and Itzhak Fishov and Jean Fourmentin-Guilbert and
Joe Fralick and Jean-Louis Giavitto and Bernard
Gleyse and Christophe Godin and Roberto Incitti and
Fran\c{c}ois K\'ep\`es and Catherine Lange and Lois
Le Sceller and Corinne Loutellier and Olivier Michel
and Franck Molina and Chantal Monnier and Ren\'e
Natowicz and Vic Norris and Nicole Orange and Helene
Pollard and Derek Raine and Camille Ripoll and
Josette Rouviere-Yaniv and Milton Saier and Paul
Soler and Pierre Tambourin and Michel Thellier and
Philippe Tracqui and Dave Ussery and Jean-Claude
Vincent and Jean-Pierre Vannier and Philippa Wiggins
and Abdallah Zemirline},
title = {Hyperstructures, genome analysis and {I}-cells},
journal = {Acta Biotheoretica},
year = {2002},
volume = 50,
page = {357--373},
note = {also appear as IHES research report M/02/95
(december 2002)},
kind = {intrevue},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/Hyperstructures.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/Hyperstructures.pdf}
}
@inbook{autran02,
author = {Giavitto, J.-L. and Godin, C. and Michel, O. and
Prusinkiewicz, P.},
title = {Modelling and Simulation of biological processes in
the context of genomics},
chapter = {``Computational Models for Integrative and
Developmental Biology''},
publisher = {Hermes},
month = jul,
year = {2002},
note = {Also republished as an high-level course in the
proceedings of the Dieppe spring school on
``Modelling and simulation of biological processes
in the context of genomics'', 12-17 may 2003,
Dieppes, France.},
kind = {chapitre},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/autran02.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/autran02.ps.gz}
}
@article{giavitto02a,
author = {Giavitto, J.-L. and Michel, O.},
title = {The Topological Structures of Membrane Computing},
journal = {Fundamenta Informaticae},
year = {2002},
volume = {49},
pages = {107--129},
kind = {intrevue},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/mgs-giavitto-michel-fundamenta-informaticae.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/mgs-giavitto-michel-fundamenta-informaticae.pdf}
}
@inproceedings{giavitto02c,
author = {Michel, O. and Giavitto, J.-L. and Cohen, J.},
title = {MGS : transformer des collections complexes pour la
simulation en biologie},
booktitle = {Journées Francophones des Langages Applicatifs
(JFLA02)},
month = jan,
year = {2002},
address = {Anglet (France)},
editor = {L. Rideau},
publisher = {INRIA},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/JFLA02.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/JFLA02.ps.gz}
}
@techreport{giavitto02R1,
author = {Giavitto, J.-L. and Godin, C. and Michel, O. and
Prusinkiewicz, P.},
title = {Computational Models for Integrative and
Developmental Biology},
institution = {LaMI -- Universit{\'e} d'{\'E}vry Val d'Essonne},
year = 2002,
number = {72-2002},
month = mar,
note = {draft version of~\cite{autran02}},
kind = {rapport},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/rt72.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/rt72.pdf}
}
@techreport{giavitto02R2,
author = {Giavitto, J.-L. and Michel, O. and Cohen, J.},
title = {Pattern-matching and Rewriting Rules for Group
Indexed Data Structures},
institution = {LaMI -- Universit{\'e} d'{\'E}vry Val d'Essonne},
year = 2002,
number = {76-2002},
month = jun,
kind = {rapport},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/rt76.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/rt76.pdf}
}
@inproceedings{giavitto02f,
author = {Giavitto, J.-L. and Michel, O.},
title = {Pattern-matching and Rewriting Rules for Group
Indexed Data Structures},
booktitle = {ACM Sigplan Workshop RULE'02},
pages = {55--66},
year = 2002,
address = {Pittsburgh},
month = oct,
publisher = {ACM},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/rule02.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/rule02.pdf}
}
@inproceedings{giavitto02d,
author = {Giavitto, J.-L. and Michel, O.},
title = {Data Structure as Topological Spaces},
booktitle = {Proceedings of the 3nd International Conference on
Unconventional Models of Computation {UMC02}},
year = {2002},
month = oct,
address = {Himeji, Japan},
volume = {2509},
note = {Lecture Notes in Computer Science},
pages = {137--150},
kind = {intconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/umc02.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/umc02.pdf}
}
@inproceedings{giavitto02b,
author = {J.-L. Giavitto and O. Michel},
title = {Accretive rules in Cayley P systems},
booktitle = {Pre-proceedings of WMC-CdeA 2002 (Workshop on
Membrane Computing, Curtea de Arges)},
month = aug,
publisher = {MolCoNet european network 2002-1},
year = {2002},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2002/PUBLIS/wmc02.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2002/wmc02.pdf}
}
@article{giavitto03a,
author = {J.-L. Giavitto and O.~Michel and F.~Delaplace},
title = {Declarative simulation of dynamicals systems : the
{$8 1/2$} programming language and its application
to the simulation of genetic networks},
journal = {BioSystems},
volume = {68},
number = {2--3},
month = {feb/march},
pages = {155--170},
year = {2003},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {
The cell as a dynamical system presents the characteristics of
having a dynamical structure. That is, the exact phase space of
the system cannot be fixed before the evolution and integrative
cell models must state the evolution of the structure jointly
with the evolution of the cell state. This kind of dynamical
systems is very challenging to model and simulate. New
programming concepts must be developed to ease their modeling
and simulation.
In this context, the goal of the MGS project is to develop an
experimental programming language dedicated to the simulation of
this kind of systems. MGS proposes a unified view on several
computational mechanisms (CHAM, Lindenmayer systems, Paun
systems, cellular automata) enabling the specification of
spatially localized computations on heterogeneous entities. The
evolution of a dynamical structure is handled through the
concept of transformation which relies on the topological
organization of the system components. An example based on the
modeling of spatially distributed biochemical networks is used
to illustrate how these notions can be used to model the spatial
and temporal organization of intracellular processes.},
equipe = {specif},
localurl = {~michel/PUBLIS/2003/PUBLIS/biosystem02bis.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2003/biosystem02bis.pdf}
}
@article{giavitto03bbis,
author = {Giavitto, Jean-Louis and Michel, Olivier},
title = {Modeling the topological organization of cellular processes},
journal = {BioSystems},
year = {2003},
number = {70},
pages = {149-163},
abstract = { The cell as a dynamical system presents the
characteristics of having a dynamical structure. That is, the exact
phase space of the system cannot be fixed before the evolution and
integrative cell models must state the evolution of the structure
jointly with the evolution of the cell state. This kind of dynamical
systems is very challenging to model and simulate. New programming
concepts must be developed to ease their modeling and simulation. In
this context, the goal of the MGS project is to develop an
experimental programming language dedicated to the simulation of
this kind of systems. MGS proposes a unified view on several
computational mechanisms (CHAM, Lindenmayer systems, Paun systems,
cellular automata) enabling the specification of spatially localized
computations on heterogeneous entities. The evolution of a dynamical
structure is handled through the concept of transformation which
relies on the topological organization of the system components. An
example based on the modeling of spatially distributed biochemical
networks is used to illustrate how these notions can be used to
model the spatial and temporal organization of intracellular
processes.},
localurl = {~michel/PUBLIS/2003/PUBLIS/biosystem02.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2003/biosystem02.pdf}
}
@inproceedings{jfla03,
author = {Cohen, Julien and Michel, Olivier and Giavitto, Jean-Louis},
title = {Filtrage et règles de réécriture sur des structures indexées par des groupes},
booktitle = {Journées Francophones des Langages Applicatifs},
year = 2003,
ibisckind = {natconf},
ibisclang = {français},
ibisccountry = {France},
abstract = {},
equipe = {specif},
localurl = {~michel/PUBLIS/2003/PUBLIS/JFLA03.ps.gz},
url = {http://www.lacl.fr/~michel/PUBLIS/2003/JFLA03.ps.gz}
}
@article{giavitto03cbis,
author = {J.-L. Giavitto and O.~Michel},
title = {Modeling the topological organization of cellular
processes},
journal = {Physics of Life},
volume = {August},
number = {3},
year = {2003},
note = {See
\url{http://www.physicsoflife.com/index.html}. Republication of \cite{giavitto03c} in the Elsevier electronic Journal ``Physics of Life'' (this journal contains selected articles that have been published in 22 contributing journals from Elsevier Science, covering Physics, Biology, Chemistry and Medicine with a focus on biological physics research).},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {},
equipe = {specif},
localurl = {},
url = {http://www1.elsevier.com/homepage/sak/physolife/archive/2003_3.htm}
}
@article{giavitto03b,
author = {Giavitto, J.-L. and Michel, O. and Cohen, J.},
title = {Pattern-matching and Rewriting Rules for Group
Indexed Data Structures},
journal = {ACM SIG{\-}PLAN Notices},
volume = {37},
number = {12},
pages = {76--87},
month = dec,
year = {2002},
issn = {0362-1340},
note = {revised version from~\cite{giavitto02f}},
equipe = {specif},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {
In this paper, we present a new framework for the definition of
various data structures (including trees and arrays) together
with a generic language of filters enabling a rule-based
programming style for functions. This framework is implemented
in an experimental language called \MGS. The underlying notions
funding our framework have a topological nature and enable to
extend the case-based definition of functions found in modern
functional languages beyond algebraic data structures.},
localurl = {~michel/PUBLIS/2003/PUBLIS/sigplan03.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2003/sigplan03.pdf}
}
@inproceedings{spicher04b,
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
title = {A topological framework for the specification and
the simulation of discrete dynamical systems},
booktitle = {Sixth International conference on Cellular Automata
for Research and Industry (ACRI'04)},
year = {2004},
volume = {3305},
page = {238--247},
series = {LNCS},
address = {Amsterdam},
month = {October},
publisher = {Springer},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {Netherlands},
abstract = {
MGS is an experimental programming language for the modeling
and the simulation of discrete dynamical systems. The modeling
approach is based on the explicit specification of the
interaction structure between the system parts. This interaction
structure is adequately described by topological notions.
The topological approach enables a unified view on several
computational mechanisms initially inspired by biological or
chemical processes (Gamma and \emph{cellular automata}).
The expressivity of the language is illustrated by the modeling
of a diffusion limited aggregation process on a wide variety of
spatial domain: from cayley graphs to arbitrary quasi-manifolds.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/acri04.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/acri04.pdf}
}
@inbook{giavitto04f,
author = {J.-L. Giavitto and O. Michel},
title = {Molecular Computational Models: Unconventional
Approaches},
chapter = {Modeling Developmental Processes in MGS},
pages = {150--189},
year = {2004},
publisher = {Idea Group Publishing},
ibisckind = {chapitre},
ibisclang = {english},
ibisccountry = {France},
abstract = {},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/Molecular_Computational_Models.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/Molecular_Computational_Models.pdf}
}
@article{giavitto04a,
author = {J.-L. Giavitto and G. Malcolm and O. Michel},
title = {Rewriting systems and the modelling of biological
systems},
journal = {Comparative and Functional Genomics},
pages = {95--99},
year = {2004},
month = feb,
volume = 5,
issue = 1,
publisher = {Wiley},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {
This note presents a short introduction to the use of rewriting
system, a notion developed in computer science, as a framework
for the modeling and the simulation of various biological
processes, especially at a cellular level.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/ComparativeFunctionalGenomics04.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/ComparativeFunctionalGenomics04.pdf}
}
@inproceedings{spicher04d,
author = {Spicher, Antoine and Michel, Olivier},
title = {Manipulations de structures topologiques dans un
langage déclaratif pour la simulation},
booktitle = {11ème Journées du GT "Animation et Simulation"
(GTAS'2004)},
year = {2004},
optvolume = {},
optnumber = {},
series = {},
address = {Reims},
month = {juin},
publisher = {AFIG et LERI, Université de Reims},
ibisckind = {colloque},
ibisclang = {français},
ibisccountry = {France},
abstract = {
MGS est un langage de programmation expérimental permettant de
manipuler des collections topologiques par des règles de
transformation. Une collection topologique est un ensemble de
valeurs muni d'une relation de voisinage. Cette approche permet
d'exprimer simplement l'état d'un système dynamique et son
évolution. La présentation du langage est faite à travers plusieurs
exemples, dont un processus de diffusion et d'agrégation sur
plusieurs quasi-variétés modélisées par des G-cartes.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/gtas04.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/gtas04.pdf}
}
@inproceedings{spicher04c,
author = {Spicher, Antoine and Michel, Olivier},
title = {Integration and pattern-matching of topological
structures in a functional language},
booktitle = {International Workshop on Implementation and
Application of Functional Languages (IFL04)},
year = {2004},
optvolume = {},
optnumber = {},
series = {},
address = {Lübeck},
month = {September},
publisher = {},
note = {draft proceedings published as a technical report of
the Institute of Computer Science of the University
of Kiel},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {Lübeck},
abstract = {MGS is an experimental programming language dedicated to the manipulation
of topological collections through rules of transformations. A topological
collection is a set of elements organized by a neighborhood relation.
This topological approach enables the extension of the case based definition
of function to several non-algebraic data types. In this paper, we show how
sophisticated data structures used to build geometric objects can be embedded
smoothly in this framework. The expressivity of the language is then illustrated
by some examples like the simulation of a diffusion limited aggregation process
on complex geometries and the computation of the maximal flow on a graph.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/IFL04.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/IFL04.pdf}
}
@techreport{giavitto04j,
author = {Giavitto, J.-L. and Michel, O. and Cohen, J. and Spicher,
A.},
title = {Computation in Space and Space in Computation},
institution = {Laboratoire des Méthodes Informatiques, UMR 8042 du CNRS},
year = {2004},
number = {103-2004},
month = may,
note = {22 p.},
ibisckind = {rapport},
ibisclang = {english},
ibisccountry = {France},
abstract = {This text and these questions were written in order to cause discussions at the Unconventional
Programming Paradigms (UPP04) international workshop held the 15--17 September
2004 at the Mont Saint-Michel, France. This workshop is dedicated to \emph{Challenges, Visions
and Research Issues for New Programming Paradigms}. We hope that this text will
stimulate fertile exchanges between the participants.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/rt-104-2004.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/rt-104-2004.pdf}
}
@techreport{michel04a,
author = {O. Michel and F. Jacquemard and J.-L. Giavitto},
title = {Three variations on the analysis of the
Needham-Schroeder Public-Key Protocol with {MGS}},
institution = {LaMI -- Université d'Evry - CNRS},
year = {2004},
number = {LaMI-98-2004},
month = may,
note = {25 p.},
ibisckind = {rapport},
ibisclang = {français},
ibisccountry = {France},
abstract = {
In this paper, we develop an analysis of the Needham-Schroeder
Public-Key Protocol (NSPK) using a P system approach. This analysis
is used to validate the protocol and exhibits, as expected, a well
known logical attack. The novelty of our approach is to use MGS, a P
system like formalism, to find the attack by a systematic state
exploration. The use of multiset rewriting has already been
advocated for the development of protocol validation tools. In this
work, we focus on the use of nested multisets (i.e. membranes). The
use of membranes enables to tight the conditions for detecting an
attack. All the three proposed version of the analysis have been
successfully implemented in MGS and we conclude the paper by a
discussion on how the MGS programs can be translated into standard P
systems.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/rt-98-2004.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/rt-98-2004.pdf}
}
@techreport{spicher04a,
author = {Spicher, Antoine and Michel, Olivier and Giavitto,
Jean-Louis},
title = {A topological framework for the specification and
the simulation of discrete dynamical systems},
institution = {LaMI},
year = 2004,
number = {LaMI-99-2004},
month = {May},
ibisckind = {rapport},
ibisclang = {english},
ibisccountry = {France},
abstract = {MGS is an experimental programming language for the modeling
and the simulation of discrete dynamical systems. The modeling
approach is based on the explicit specification of the interaction structure
between the system parts. This interaction structure is adequately
described by topological notions. The topological approach enables a
unified view on several computational mechanisms initially inspired by
biological or chemical processes (Gamma and the CHAM, Lindenmayer
systems, P systems and cellular automata). The expressivity of the language
is illustrated by the modeling of a diffusion limited aggregation
process on a wide variety of spatial domain: from cayley graphs to arbitrary
manifolds.},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/rt-99-2004.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/rt-99-2004.pdf}
}
@article{giavitto04k,
author = {Giavitto, J.-L. and Michel, O. and Banâtre, J.-P and Fradet, P.},
title = {Modèles de programmation non-conventionnels},
journal = {Technique et Science Informatique},
year = {2004},
volume = {23},
pages = {177--186},
note = {Compte-rendu de l'atelier international UPP'04.},
ibisckind = {natrevue},
ibisclang = {français},
ibisccountry = {France},
abstract = {},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/tsi-2004.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/tsi-2004.pdf}
}
@proceedings{giavitto04h,
title = {Proceedings of EU-NSF Strategic Research Workshop on
Unconventional Programming Paradigms (UPP'04)},
year = {2004},
editor = {Giavitto, J.-L. and Banâtre, J.-P and Fradet, P. and
Michel, O.},
address = {Mont Saint-Michel},
optmonth = sep,
organization = {ERCIM -- NFS},
publisher = {ERCIM,\url{http://www.ercim.org/EU-NSF/UPP04-proceedings.pdf}},
note = {The final proceedings will be published in LNCS.},
ibisckind = {editeur},
ibisclang = {english},
ibisccountry = {France},
abstract = {},
kind = {editeur},
equipe = {specif}
}
@inproceedings{michel04b,
author = {O. Michel and F. Jacquemard},
title = {An Analysis of the {N}eedham-{S}chroeder Public-Key
Protocol with {MGS}},
booktitle = {Preproceedings of the Fifth workshop on Membrane
Computing (WMC5)},
pages = {295--315},
year = {2004},
editor = {G. Mauri and G. Paun and C Zandron},
month = jun,
publisher = {EC MolConNet - Universita di Milano-Bicocca},
ibisckind = {natconf},
ibisclang = {english},
ibisccountry = {Italy},
abstract = {In this paper, we develop an analysis of the Needham-Schroeder
Public-Key Protocol in the framework of membrane
computing. This analysis is used to validate the protocol and
exhibits, as expected, a well known logical attack. The novelty
of our approach is to use multiset rewriting in a nest of
membranes. The use of membranes enables to tight the conditions
for detecting an attack.
The approach has been validated by developing a full
implementation for several versions of the analysis.},
kind = {natconf},
equipe = {specif},
localurl = {~michel/PUBLIS/2004/PUBLIS/wmc-04.ps},
url = {http://www.lacl.fr/~michel/PUBLIS/2004/wmc-04.ps}
}
@inproceedings{ea05,
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
title = {Algorithmic self-assembly by accretion and by carving in MGS},
booktitle = {7th International Conference on Artificial Evolution},
year = {2005},
pages = {189-200},
localurl = {~michel/PUBLIS/2005/PUBLIS/ea05.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/ea05.pdf},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {France},
abstract = { We report the use of MGS, a declarative and rule-based
language, for the modeling of various self-assembly processes.
The approach is illustrated on the fabrication of a fractal
pattern, a Sierpinsky triangle, using two approaches: by
\emph{accretive growth} and by \emph{carving}. The notion of
topological collections available in MGS enables the easy and
concise modeling of self-assembly processes on various lattice geometries
as well as more arbitrary constructions of multi-dimensional
objects.}
}
@inproceedings{giavitto05e,
author = {Michel, Olivier and Banâtre, Jean-Pierre and Fradet, Pascal and Giavitto, Jean-Louis},
title = {Challenging Questions for the Rationals of
Non-Classical Programming Languages},
booktitle = {The Grand Challenge in Non-Classical Computation},
year = {2005},
address = {The King's Manor, York, United Kingdom},
month = {18-19 April},
organization = {University of York and Microsoft Research},
note = {(an extended version will be published in the
Journal of Unconventional Computing)},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {England},
abstract = {},
localurl = {~michel/PUBLIS/2005/PUBLIS/gc2005.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/gc2005.pdf}
}
@inproceedings{iccs05,
author = {Spicher, Antoine and Michel, Olivier},
title = {Using Rewriting Techniques in the Simulation of Dynamical Systems: Application to the Modeling of Sperm Crawling},
booktitle = {Fifth International Conference on Computational Science (ICCS'05)},
pages = {820--827},
year = {2005},
volume = {I},
number = {LNCS 3514},
localurl = {~michel/PUBLIS/2005/PUBLIS/iccs.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/iccs.pdf},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {USA},
abstract = {
Rewriting system (RS) are a formalism widely used in computer
science. However, such a formalism can also be used to specify
executable models of dynamical systems (DS) by allowing the
specification of the evolution laws of the systems in a local
manner.
The main drawback of RS is that they are well understood and well
known only for terms (a tree-like structure) and that their
expressivity is not enough for the representation of complex
organizations that can be found in DS.
We propose a framework based on topological notion to extend the
notion of RS on more sophisticated structures; the corresponding
concepts are validated through the development of an experimental
programming language, MGS, dedicated to the simulation of DS. We
show how the MGS rewriting system can be used to specify complex
dynamical systems and illustrate it with the simulation of the
motility of the nematode's sperm cell. }
}
@inproceedings{ipcat05,
author = {Spicher, Antoine and Michel, Olivier},
title = {Declarative modeling of a neurulation-like process},
booktitle = {Sixth International Workshop on Information Processing in Cells and Tissues},
year = {2005},
localurl = {~michel/PUBLIS/2005/PUBLIS/ipcat05_spicher_michel_CRV.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/ipcat05_spicher_michel_CRV.pdf},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {England},
abstract = {
MGS is an experimental programming language dedicated to the modeling and
the simulation of a special kind of discrete dynamical
systems. \emph{Dynamical systems with a dynamical structure} (or DS$^2$) arise
when the state space is not fixed \emph{a priori} but is jointly computed with
the current state during the simulation. In this case the evolution function
is often given through local rules that drive the interaction between some
system components. MGS offers a new kind of data structure, \emph{topological
collections}, to describe the state of a dynamical system, and
\emph{transformations} to express local and discrete evolution laws. These two
notions permit an easy specification of DS$^2$.
We propose in this paper a presentation of the MGS language and its main
contributions. We show that various topological collections can be unified
using concepts developped in combinatorial algebraic topology: \emph{cellular
complexes} and \emph{topological chains}. Then we apply the notions brought by
MGS to model and simulate the first step towards the simulation of the
neurulation process where a sheet of cell evolves to a neural tube. It is a
direct description of the modification of the topology of an arbitrary
structure expressed in terms of local discrete evolution laws.}
}
@inbook{michel05a,
author = {O. Michel and F. Jacquemard},
title = {An Analysis of a Public-Key Protocol with Membranes},
booktitle = {Applications of Membrane Computing},
pages = {283--302},
year = {2005},
editor = {G. Ciobanu and G. P{\u a}un and . J. P{\'e}rez-Jim{\'e}nez},
series = {Natural Computing Series},
annote = {(442 + viii pages)},
publisher = {Springer Verlag},
ibisckind = {chapter},
ibisclang = {english},
ibisccountry = {},
abstract = {
In this paper, we develop an analysis of the Needham-Schroeder
Public-Key Protocol in the framework of membrane
computing. This analysis is used to validate the protocol and
exhibits, as expected, a well known logical attack. The novelty
of our approach is to use multiset rewriting in a nest of
membranes. The use of membranes enables to tight the conditions
for detecting an attack.
The approach has been validated by developing a full
implementation for several versions of the analysis.},
equipe = {specif},
localurl = {~michel/PUBLIS/2005/PUBLIS/nspk-05.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/nspk-05.pdf}
}
@proceedings{giavitto05b,
title = {Proceedings of EU-NSF Strategic Research Workshop on the Unconventional Programming
Paradigms (UPP'04)},
year = {2004},
editor = {Banâtre, J.-P and Fradet, P. and Giavitto, J.-L. and Michel, O.},
address = {Mont Saint-Michel, France},
month = sep,
organization = {ERCIM -- NSF},
publisher = {Springer Verlag},
series = {LNCS},
volume = {3566},
note = {Revised, selected and invited papers. 367 p. ISBN:
3-540-27884-2. \url{http://www.springeronline.com/3-540-27884-2}},
ibisckind = {editeur},
ibisclang = {english},
ibisccountry = {France},
abstract = {},
equipe = {specif},
localurl = {},
url = {http://www.springer.com/france/home/generic/search/results?SGWID=7-40109-22-56489535-0}
}
@inproceedings{giavitto05z,
author = {Giavitto, Jean-Louis and Michel, Olivier and Cohen, Julien and Spicher, Antoine},
title = {Computation in Space and Space in Computation},
booktitle = {Unconventional Programming Paradigms (UPP'04) },
pages = {137-152},
year = {2005},
editor = {Banâtre, J.-P and Fradet, P. and Giavitto, J.-L. and Michel, O.},
volume = {3566},
series = {LNCS},
organization = {ERCIM-- NSF},
publisher = {Springer Verlag},
ibisckind = {intconf},
ibisclang = {english},
ibisccountry = {France},
abstract = {},
localurl = {~michel/PUBLIS/2005/PUBLIS/upp04-version-finale-lncs.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2005/upp04-version-finale-lncs.pdf}
}
@article{spicher05bio,
author = {Spicher, Antoine and Michel, Olivier},
title = {Declarative modeling of a neurulation-like process},
journal = {BioSystems},
year = {2006},
pages = {281-288},
volume = {87},
month = feb,
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {
{MGS} is an experimental programming language dedicated to the
modeling and the simulation of a special kind of discrete dynamical
systems. \emph{Dynamical systems with a dynamical structure} (or
DS2) arise when the state space is not fixed \emph{a priori} but is
jointly computed with the current state during the simulation. In
this case the evolution function is often given through local rules
that drive the interaction between some system components. {MGS}
offers a new kind of data structure, \emph{topological collections},
to describe the state of a dynamical system, and a new kind of
control structure, \emph{transformations}, to express local and
discrete evolution laws. These two notions permit an easy
specification of DS2.
We propose in this paper a presentation of the {MGS} language and its
main contributions. We show that various topological collections can
be unified using concepts developed in combinatorial algebraic
topology: \emph{cellular complexes} and \emph{topological
chains}. Then we apply the notions brought by {MGS} to model and
simulate the first step towards the simulation of the neurulation
process in developmental biology where a sheet of cells evolves to a
neural tube. It is a direct description of the modification of the
topology of an arbitrary structure expressed in terms of local
discrete evolution laws.},
equipe = {specif},
localurl = {~michel/PUBLIS/2006/PUBLIS/biosystem06.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2006/biosystem06.pdf}
}
@inbook{bordeaux06,
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
title = {Rewriting and Simulation - Application to the Modeling of the Lambda Phage Switch},
chapter = {Modeling of the Lambda Phage Switch},
publisher = {Genopole},
year = {2006},
volume = {Modélisation de systèmes biologiques complexes dans le contexte de la génomique},
number = {5},
ibisckind = {colloque},
ibisclang = {english},
ibisccountry = {France},
abstract = {A modeling of the Lambda Phage Switch using the MGS language.},
localurl = {~michel/PUBLIS/2006/PUBLIS/phage-spicher-michel.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2006/phage-spicher-michel.pdf}
}
@article{ijuc06,
author = {Michel, Olivier and Banâtre, Jean-Pierre and Fradet, Pascal and Giavitto, Jean-Louis},
title = {Challenging Questions for the Rationales of Non-Classical Programming Languages},
journal = {International Journal of Unconventional Computing},
year = {2006},
note = {accepted for publishing},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {In this position paper, we question the rationale behind the design
of unconventional programming languages. Our questions
are classified in four categories: the sources of inspiration for
new computational models, the process of developing a program,
the forms and the theories needed to write and understand nonclassical
programs and finally the new computing media and the
new applications that drive the development of new programming
languages.},
localurl = {~michel/PUBLIS/2006/PUBLIS/final-ijuc-michel-banatre-fradet-giavitto-position-paper.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2006/final-ijuc-michel-banatre-fradet-giavitto-position-paper.pdf}
}
@inproceedings{jfla06,
author = {Spicher, Antoine and Michel, Olivier},
title = {Stratégie d'application stochastique de règles de réécritures dans le langage {MGS}},
booktitle = {Journées Francophones des Langages Applicatifs},
year = {2006},
publisher = {INRIA},
ibisckind = {natconf},
ibisclang = {français},
ibisccountry = {France},
abstract = {},
localurl = {~michel/PUBLIS/2006/PUBLIS/jfla06.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2006/jfla06.pdf}
}
@inproceedings{ifl07,
author = {Michel, Olivier and Giavitto, Jean-Louis},
title = {Incremental extension of a domain specific language interpreter},
booktitle = {19th International Symposium on Implementation and Application of Functional Languages},
year = {2007},
address = {Freiburg, Germany},
month = {27--29 September},
abstract = {We have developed an interpreter for the domain-specific
language MGS using OCAML as the implementation language. In this
third implementation of MGS, we wanted to provide the end-user with
easy incremental addition of new data structures and their
associated functions to the language. We detail in this paper our
solution, in a functional setting, which is based on techniques
similar to those found in aspect-oriented programming.},
laclkind = {intconf},
lacllang = {english},
laclcountry = {Germany},
localurl = {~michel/PUBLIS/2007/PUBLIS/ifl07.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2007/ifl07.pdf}
}
@article{tsijfla07,
author = {Spicher, Antoine and Michel, Olivier},
title = {Représentation et manipulation de structures topologiques dans un langage fonctionnel},
journal = {Technique et Science Informatique},
year = {2007},
ibisckind = {natrevue},
ibisclang = {français},
ibisccountry = {France},
localurl = {~michel/PUBLIS/2007/PUBLIS/tsijfla07.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2007/tsijfla07.pdf}
}
@article{spicher07bio,
author = {Spicher, Antoine and Michel, Olivier and Cieslak, Mikolaj and Giavitto, Jean-Louis and Prusinkiewicz, Przemyslaw},
title = {Stochastic P Systems and the Simulation of Biochemical Processes with Dynamic Compartments},
journal = {BioSystems},
year = {2008},
pages = {458-472},
volume = {91},
number = {3},
month = {March},
ibisckind = {intrevue},
ibisclang = {english},
ibisccountry = {},
abstract = {
We introduce a sequential rewriting strategy for P systems based on
Gillespie's stochastic simulation algorithm, and apply the resulting
formalism of stochastic P systems to simulate biochemical processes
in dynamically changing, nested compartments. Stochastic P systems
have been implemented using the spatially explicit programming
language {\mgs}. Implementation examples include models of the
Lotka-Volterra auto-catalytic system, and the life cycle of the
Semliki Forest virus.},
equipe = {specif},
localurl = {~michel/PUBLIS/2008/PUBLIS/biosystem08.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2008/biosystem08.pdf}
}
@inproceedings{GIAVITTO:2008:HAL-00340504:1,
title = {Topological Structure of Interactions},
author = {Giavitto, Jean-Louis and Michel, Olivier},
language = {{A}nglais},
affiliation = {{I}nformatique, {B}iologie {I}nt{\'e}grative et {S}yst{\`e}mes {C}omplexes - {IBISC} - {CNRS} : {FRE}3190 - {U}niversit{\'e} d'{E}vry-{V}al d'{E}ssonne },
booktitle = {1st {E}uropean {W}orkshop on {C}orrelations in {C}omputer {S}cience 1st {E}uropean {W}orkshop on {C}orrelations in {C}omputer {S}cience },
pages = {({E}lec. {P}roc.) },
address = {{V}ielsalm {B}elgique },
audience = {non sp{\'e}cifi{\'e}e },
year = {2008},
url = {http://hal.archives-ouvertes.fr/hal-00340504/en/}
}
@inproceedings{Norris2008,
author = {Vic Norris and Abdallah Zemirline and Patrick Amar and
Pascal Ballet and Eshel Ben Jacob and Gilles Bernot and
Guillaume Beslon and Eric Fanchon and Jean-Louis Giavitto and
Nicolas Glade and Patrick Greussay and Yohann Grondin and
James A. Foster and Guillaume Hutzler and and Francois
Kepes and Olivier Michel and Gradimir Misevic and Franck
Molina and Jacqueline Signorini and Pasquale Stano and
Alain Thierry},
title = {From bioputing to bactoputing : computing with bacteria},
booktitle = {Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics},
year = {2008},
month = apr,
pages = {123--150}
}
@inproceedings{iterlink08,
author = {Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine},
title = {Spatial Organization of the Chemical Paradigm and the Specification of Autonomic Systems},
booktitle = {Software-Intensive Systems},
year = {2008},
localurl = {~michel/PUBLIS/2008/PUBLIS/interlink08.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2008/interlink08.pdf},
ibisckind = {intconf},
abstract = {The chemical paradigm is an unconventional programming
paradigm well fitted to the high-level specification of
parallel systems. Based on the fixed point iterations
of local rules, its use has been advocated for the
programming of autonomic and amorphous systems. However,
this model lacks an explicit handling of spatial
relationships. In this contribution, we first show how
the chemical paradigm can be extended beyond multisets
to arbitrary topological collections. Topological
collections handle in a uniform way sophisticated data
structures required in algorithmics as well as
distributed data structures needed for the programming
of autonomic or amorphous systems. Then we adapt a
well-known result on multiset ordering to the more
general case of topological collections. Well-founded
ordering on topological collection can be used to prove
the termination of the fixed point iteration of local
rules.}
}
@inproceedings{GIAVITTO:2008:HAL-00340505:1,
title = {Topologie combinatoire et programmation},
author = {Giavitto, Jean-Louis and Michel, Olivier},
language = {{F}ran{\c{c}}ais},
affiliation = {{I}nformatique, {B}iologie {I}nt{\'e}grative et {S}yst{\`e}mes {C}omplexes - {IBISC} - {CNRS} : {FRE}3190 - {U}niversit{\'e} d'{E}vry-{V}al d'{E}ssonne },
booktitle = {{R}encontre toulousaine graphes et topologie},
pages = {n.a. },
address = {{T}oulouse {F}rance },
audience = {non sp{\'e}cifi{\'e}e },
year = {2008},
url = {http://hal.archives-ouvertes.fr/hal-00340505/en/}
}
@article{naco09,
author = {Michel, Olivier and Spicher, Antoine and Giavitto, Jean-Louis},
title = {Rule-based programming for integrative biological modeling -- Application to the modeling of the lambda phage genetic switch},
abstract = {Systems biology aims at integrating processes at various time and spatial
scales into a single and coherent formal description to allow computer modeling. In
this context, we focus on rule-based modeling and its integration in the domain-specific
language MGS. Through the notions of topological collections and transformations, MGS
allows the modeling of biological processes at various levels of description. We validate
our approach through the description of various models of the genetic switch of the lambda
phage, from a very simple biochemical description of the process to an individual-based
model on a Delaunay graph topology. This approach is a first step into providing the
requirements for the emerging field of spatial systems biology which integrates spatial
properties into systems biology.},
journal = {Natural Computing},
year = {2009},
pages = {865--889},
volume = {8},
number = {4},
month = {december},
note = {Published online: 12 November 2008},
doi = {10.1007/s11047-008-9105-9},
url = {http://www.lacl.fr/~michel/PUBLIS/2009/naco09.pdf}
}
@inproceedings{saso09,
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
title = {Spatial Computing as Intensional Data Parallelism},
booktitle = {Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems - Spatial Computing Workshop},
year = {2009},
address = {San Franciso, United States},
month = {14--18 September},
abstract = {In this paper, we show that various concepts and tools developed in the 90's in the field of data-parallelism provide a relevant spatial programming framework. It allows high level spatial computation specifications to be translated into efficient low-level operations on processing units. We provide some short examples to illustrate this statement.},
laclkind = {intconf},
lacllang = {english},
laclcountry = {USA},
localurl = {~michel/PUBLIS/2009/PUBLIS/spatial-computing09.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2009/spatial-computing09.pdf}
}
@inproceedings{MUZY:2010:HAL-00465463:1,
title = { {A}ctivity {R}egions for the {S}pecification of {D}iscrete {E}vent {S}ystems},
author = {{M}uzy, {A}lexandre and {T}ouraille, {L}uc and {V}angheluwe,
{H}ans and {M}ichel, {O}livier and {K}aba
{T}raor{\'e}, {M}amadou and {R}.{C}. {H}ill,
{D}avid},
abstract = {{T}he common view on modeling and simulation of dynamic
systems is to focus on the specification of the
state of the system and its transition
function. {A}lthough some interesting challenges
remain to efficiently and elegantly support this
view, we consider in this paper that this problem is
solved. {I}nstead, we propose here to focus on a new
point of view on dynamic system specifications: the
activity exhibited by their discrete event
simulation. {W}e believe that such a viewpoint
introduces a new way for analyzing, modeling and
simulating systems. {W}e first start with the
definition of the key notion of activity for the
specification of a specific class of dynamic system,
namely discrete event systems. {T}hen, we refine
this notion to characterize activity regions in
time, in space, in states and in hierarchical
component-based models. {E}xamples are given to
illustrate and stress the importance of this
notion.},
age = {{A}nglais},
affiliation = {{L}ieux, {I}dentit{\'e}s, e{S}paces, {A}ctivit{\'e}s -
{LISA} - {U}niversit{\'e} {P}ascal {P}aoli - {CNRS}
: {UMR}6240 - {L}aboratoire d'{I}nformatique, de
{M}od{\'e}lisation et d'optimisation des
{S}yst{\`e}mes - {LIMOS} - {CNRS} : {UMR}6158 -
{U}niversit{\'e} d'{A}uvergne - {C}lermont-{F}errand
{I} - {U}niversit{\'e} {B}laise {P}ascal -
{C}lermont-{F}errand {II} - {I}nstitut
{F}ran{\c{c}}ais de {M}{\'e}canique {A}vanc{\'e}e -
{S}chool of {C}omputer {S}cience - {SOCS} -
{M}c{G}ill {U}niversity - {L}aboratoire
d'{A}lgorithmique {C}omplexit{\'e} et {L}ogique -
{LACL} - {CNRS} : {FRE}2673 - {U}niversit{\'e}
{P}aris {XII} {V}al de {M}arne },
booktitle = {{S}pring {S}imulation {M}ulti-{C}onference {S}ymposium
{O}n {T}heory of {M}odeling and {S}imulation -
{DEVS} {I}ntegrative {M}\&{S} {S}ymposium
({DEVS}'10) },
pages = {{A}ccepted for publication },
address = {{\'E}tats-{U}nis d'{A}m{\'e}rique },
note = {{ACM}, {SCS} {CNRS} },
audience = {internationale },
year = {2010},
url = {http://www.lacl.fr/~michel/PUBLIS/2010/devs2010.pdf}
}
@inbook{dubi10,
chapter = {Interaction-based simulations for Integrative Spatial Systems Biology},
pages = {195-231},
title = {Understanding the dynamics of biological systems},
publisher = {Springer},
year = {2011},
editor = {Springer},
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
owner = {michel},
timestamp = {2011.04.15},
url = {http://www.lacl.fr/~michel/PUBLIS/2010/ibss.pdf}
}
@inproceedings{icgt10,
title = {Declarative Mesh Subdivision Using Topological Rewriting in MGS},
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
year = {2010},
pages = {298--313},
volume = {6372},
series = {LNCS},
month = sep,
abstract = {Mesh subdivision algorithms are usually specified
informally using graphical schemes defining local
mesh refinements. These algorithms are then
implemented efficiently in an imperative
framework. The implementation is cumbersome and
implies some tricky indices management. Smith et
al. (2004) asks the question of the declarative
programming of such algorithms in an index-free
way. In this paper, we positively answer this
question by presenting a rewriting framework where
mesh refinements are described by simple rules. This
framework is based on a notion of topological chain
rewriting. Topological chains generalize the notion
of labeled graph to higher dimensional objects. This
framework has been implemented in the domain
specific language MGS. The same generic approach
has been used to implement Loop as well as
Butterfly, Catmull-Clark and Kobbelt subdivision
schemes.},
booktitle = {International Conference on Graph Transformation},
pages = {{A}ccepted for publication },
address = {The Netherlands},
url = {http://www.lacl.fr/~michel/PUBLIS/2010/icgt2010.pdf}
}
@inproceedings{scw10,
author = {Bigo, Louis and Spicher, Antoine and Michel, Olivier},
title = {Spatial Programming for Music Representation and Analysis},
booktitle = {Fourth IEEE International Conference on Self-Adaptive and Self-Organizing Systems - Spatial Computing Workshop},
year = {2010},
address = {Budapest, Hungary},
month = {27 September},
abstract = {In this paper, we show how some musical objects and some algorithmic problems arising in musical theory can be rephrased in spatial terms. This leads to the development of meaningful spatial representations and of efficient spatial programs. The corresponding developments have been implemented in MGS, a rule-based spatial programming language.},
laclkind = {intconf},
lacllang = {english},
laclcountry = {USA},
localurl = {~michel/PUBLIS/2010/PUBLIS/scw10.pdf},
url = {http://www.lacl.fr/~michel/PUBLIS/2010/scw10.pdf}
}
@inproceedings{Bigo11b,
author = {Bigo, Louis and Spicher, Antoine and Michel, Olivier},
title = {Two Representations of Music Computed with a Spatial Programming Language},
booktitle = {New Worlds of Computation 2011},
address = {Orl\'eans, France},
month = {Mai},
year = {2011},
url = {http://www.lacl.fr/~michel/PUBLIS/2011/nwc11.pdf}
}
@inproceedings{scsc11,
title = {Interaction Based Simulation of Dynamical System with a Dynamical Structure (DS)2 in MGS},
author = {Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine},
year = {2011},
month = jun,
abstract = {We present the domain specific programming language MGS
and its approach to the specification of dynamical
systems with a dynamical structure or (DS)2. MGS
stands 'encore un Modele General de Simulation',
that is, 'Yet another geneeral model of
simulation'. Its declarative approach is based on
the notions of chains and cochains well studied in
algebraic topology. A careful discussion of the
design goals lead us to relax some of the
constraints on these mathematical structures to
represent in a uniform way various data structures
and transformations. In particular, our
computational notion of transformation relies on a
rewriting mechanism encompassing the usual notions
of set, string and term rewriting. These notions are
illustrated on two examples involving the implicit
computation of a time varying neighborhood: the
simulation of the trajectories of floocking birds
and the growth of an epithelial tissue. The second
example illustrates also the compositionality
achieved by the declarative framework. The MGS
concepts have been further validated on several
large scale simulations of complex biological
systems.},
booktitle = {Summer Computer Simulation Conference},
pages = {99-106},
issn = {978-1-61782-950-5},
address = {The Netherlands},
url = {http://www.lacl.fr/~michel/PUBLIS/2011/scsc11.pdf}
}
@article{taas2011,
author = {Beal, Jacob and Michel, Olivier and Schultz, Ulrik Pagh},
title = {Spatial Computing: Distributed Systems That Take Advantage of Our Geometric World},
journal = {ACM Trans. Auton. Adapt. Syst.},
issue_date = {June 2011},
volume = {6},
issue = {2},
month = {June},
year = {2011},
issn = {1556-4665},
pages = {11:1--11:3},
articleno = {11},
numpages = {3},
doi = {http://doi.acm.org/10.1145/1968513.1968514},
acmid = {1968514},
publisher = {ACM},
address = {New York, NY, USA},
url = {http://www.lacl.fr/~michel/PUBLIS/2011/taas.pdf}
}
@article{norris2011,
author = {Norris, Vic and Zemirline, Abdallah and Amar, Patrick
and Audinot, Jean and Ballet, Pascal and Ben-Jacob,
Eshel and Bernot, Gilles and Beslon, Guillaume and
Cabin, Armelle and Fanchon, Eric and Giavitto,
Jean-Louis and Glade, Nicolas and Greussay, Patrick
and Grondin, Yohann and Foster, James and Hutzler,
Guillaume and Jost, Jörgen and Kepes, Francois and
Michel, Olivier and Molina, Franck and Signorini,
Jacqueline and Stano, Pasquale and Thierry, Alain},
title = {Computing with bacterial constituents, cells and
populations: from bioputing to bactoputing},
journal = {Theory in Biosciences},
publisher = {Springer Berlin / Heidelberg},
issn = {1431-7613},
keyword = {Biomedical and Life Sciences},
pages = {1-18},
note = {10.1007/s12064-010-0118-4},
abstract = {The relevance of biological materials and processes to
computing (bioputing) has been explored for
decades. These materials include DNA, RNA and
proteins, while the processes include transcription,
translation, signal transduction and
regulation. Recently, the use of bacteria themselves
as living computers has been explored but this use
generally falls within the classical paradigm of
computing. Computer scientists, however, have a
variety of problems to which they seek solutions,
while microbiologists are having new insights into the
problems bacteria are solving and how they are solving
them. Here, we envisage that bacteria might be used
for new sorts of computing. These could be based on
the capacity of bacteria to grow, move and adapt to a
myriad different fickle environments both as
individuals and as populations of bacteria plus
bacteriophage. New principles might be based on the
way that bacteria explore phenotype space via
hyperstructure dynamics and the fundamental nature of
the cell cycle. This computing might even extend to
developing a high level language appropriate to using
populations of bacteria and bacteriophage. Here, we
offer a speculative tour of what we term bactoputing,
namely the use of the natural behaviour of bacteria
for calculating.},
year = 2011,
url = {http://www.lacl.fr/~michel/PUBLIS/2011/tib.pdf}
}
@inproceedings{susan12,
title = {Gardening Cyber-Physical Systems},
author = {Stepney, Susan and Diaconescu, Ada and Doursat,
Ren\'e and Giavitto, Jean-Louis and Kowaliw, Taras
and Leyser, Ottoline and MacLennan, Bruce and
Michel, Olivier and Miller, Julian F. and Nikolic,
Igor and Spicher, Antoine and Teuscher, Christof and
Tufte, Gunnar and Vico, Francisco J. and Yamamoto,
Lidia},
year = {2012},
month = jun,
booktitle = {Unconventional Computation \& Natural Computation},
pages = {Abstract},
address = {France},
url = {http://www.lacl.fr/~michel/PUBLIS/2012/grocyphy.pdf}
}
@inproceedings{scw12,
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
title = {Arbitrary nesting of spatial computing},
booktitle = {Spatial Computing Workshop 2012 at AAMAS},
year = {2012},
address = {Valencia, Spain},
month = {June},
organization = {},
publisher = {AAMAS},
url = {http://www.lacl.fr/~michel/PUBLIS/2012/scw12.pdf}
}
@article{tcj2012,
author = {Beal, Jacob and Dulman, Stefan and Michel, Olivier and Spicher, Antoine},
title = {Better Living Through Manifold Geometry},
journal = {{T}he {C}omputer {J}ournal - Special issue on {S}patial {C}omputing},
year = {2012},
month = {dec},
note = {Editorial introduction},
url = {http://www.lacl.fr/~michel/PUBLIS/2012/TCJ12-SpatialComputing-Editorial.pdf}
}
@inproceedings{ucnc12,
hal_id = {hal-00769284},
url = {http://hal.archives-ouvertes.fr/hal-00769284},
title = {{Spatial Computing in MGS}},
author = {Spicher, Antoine and Michel, Olivier and Giavitto, Jean-Louis},
abstract = {{Abstract. This short paper motivates and introduces the tutorial on MGS and spatial computing presented at UCNC 2012.}},
language = {Anglais},
affiliation = {Laboratoire d'Algorithmique Complexit{\'e} et Logique - LACL , MUTANT - Inria Paris-Rocquencourt , Sciences et Technologies de la Musique et du Son - STMS},
booktitle = {{Unconventional Computation and Natural Computation}},
publisher = {Springer},
pages = {63-69},
address = {Orl{\'e}ans, France},
journal = {Lecture notes in computer science},
volume = {7445},
editor = {J{\'e}r{\^o}me Durand-Lose, Nata{\v s}a Jonoska },
note = {Additional material is available from http://www.spatial-computing.org/mgs/tutorial },
audience = {internationale },
doi = {10.1007/978-3-642-32894-7\_7 },
year = {2012},
pdf = {http://www.lacl.fr/~michel/PUBLIS/2012/ucnc12.pdf}
}
@article{ijuc13,
author = {Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine},
title = {Unconventional and Nested Computations in Spatial Computing},
journal = {International Journal of Unconventional Computing},
year = {2013},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/ijuc13.pdf},
optkey = {},
optvolume = {},
optnumber = {},
optpages = {},
optmonth = {},
optnote = {},
optannote = {}
}
@incollection{mcm13,
year = {2013},
isbn = {978-3-642-39356-3},
booktitle = {Mathematics and Computation in Music},
volume = {7937},
series = {Lecture Notes in Computer Science},
editor = {Yust, Jason and Wild, Jonathan and Burgoyne, JohnAshley},
doi = {10.1007/978-3-642-39357-0_3},
title = {Computation and Visualization of Musical Structures in Chord-Based Simplicial Complexes},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/mcm13.pdf},
publisher = {Springer Berlin Heidelberg},
keywords = {MGS; simplicial complexes; generalized Tonnetze; compliance; Hexachord; chord spaces},
author = {Bigo, Louis and Andreatta, Moreno and Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine},
pages = {38-51}
}
@inbook{mewintro13,
author = {Doursat, Ren\'e and Sayama, Hiroki and Michel, Olivier},
editor = {Doursat, Ren\'e and Sayama, Hiroki and Michel, Olivier},
title = {Morphogenetic Engineering},
chapter = {Morphogenetic Engineering: Reconciling self-organization and architecture},
publisher = {Springer},
year = {2013},
series = {Understanding complex systems},
month = jan,
pages = {1--24},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/Doursat_Sayama_Michel_2012_MorphEng_Chapter1.pdf}
}
@inbook{mewchap13,
author = {Spicher, Antoine and Giavitto, Jean-Louis and Michel, Olivier},
editor = {Doursat, Ren\'eand Sayama, Hiroki and Michel, Olivier},
title = {Morphogenetic Engineering},
chapter = {Interaction-Based Modeling of Morphogenesis},
publisher = {Springer},
year = {2013},
series = {Understanding Complex Systems},
month = jan,
pages = {409--440},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/interaction-based_modeling_of_morphogenesis.pdf}
}
@book{mewed13,
editor = {Doursat, Ren\'e and Sayama, Hiroki and Michel, Olivier},
title = {Morphogenetic Engineering},
publisher = {Springer},
year = {2013},
month = jan,
series = {Understanding complex systems},
pages = {517}
}
@article{mewreview2013,
year = {2013},
month = {September},
issn = {1567-7818},
journal = {Natural Computing},
doi = {10.1007/s11047-013-9398-1},
title = {A review of morphogenetic engineering},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/Doursat_Sayama_Michel_2013_MorphEng_review.pdf},
publisher = {Springer Netherlands},
keywords = {Agent-based modeling; Artificial life; Collective construction; Complex systems; Evolutionary development; Generative grammars; Morphogenesis; Self-organization; Swarm robotics; Systems engineering},
author = {Doursat, Ren\'e and Sayama, Hiroki and Michel, Olivier},
pages = {1-19},
language = {English}
}
@inproceedings{Potier:2013:TCA:2486092.2486136,
author = {Potier, Martin and Spicher, Antoine and Michel, Olivier},
title = {Topological Computation of Activity Regions},
booktitle = {Proceedings of the 2013 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation},
series = {SIGSIM-PADS '13},
year = {2013},
isbn = {978-1-4503-1920-1},
location = {Montréal, Québec, Canada},
pages = {337--342},
numpages = {6},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/pads13.pdf},
doi = {10.1145/2486092.2486136},
acmid = {2486136},
publisher = {ACM},
address = {New York, NY, USA},
keywords = {activity tracking, mgs programming language, rule-based modeling and simulation, spatial computing, topology of interactions}
}
@article{scs13,
author = {Muzy, Alexandre and Varenne, Franck and Zeigler, Bernard P. and Caux, Jonathan and Coquillard, Patrick and Touraille, Luc and Prunetti, Dominique and Caillou, Philippe and Michel, Olivier and Hill, David RC},
title = {Refounding of Activity Concept? Towards a Federative Paradigm for Modeling and Simulation},
journal = {SIMULATION: Transactions of The Society for Modeling and Simulation International},
year = {2013},
month = {Feb},
volume = {89},
number = {2},
pages = {156-177},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/10.1177_0037549712457852.pdf}
}
@incollection{mcm13b,
year = {2013},
isbn = {978-3-642-39356-3},
booktitle = {Mathematics and Computation in Music},
volume = {7937},
series = {Lecture Notes in Computer Science},
editor = {Yust, Jason and Wild, Jonathan and Burgoyne, JohnAshley},
doi = {10.1007/978-3-642-39357-0_3},
title = {Computation and Visualization of Musical Structures in Chord-Based Simplicial Complexes},
url = {http://www.lacl.fr/~michel/PUBLIS/2013/mcm13.pdf},
publisher = {Springer Berlin Heidelberg},
keywords = {MGS; simplicial complexes; generalized Tonnetze; compliance; Hexachord; chord spaces},
author = {Bigo, Louis and Andreatta, Moreno and Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine},
pages = {38-51}
}
@article{doi:10.1021/acssynbio.5b00246,
author = {Pascalie, Jonathan and Potier, Martin and Kowaliw, Taras and Giavitto, Jean-Louis and Michel, Olivier and Spicher, Antoine and Doursat, René},
title = {Developmental Design of Synthetic Bacterial Architectures by Morphogenetic Engineering},
journal = {ACS Synthetic Biology},
volume = {5},
number = {8},
pages = {842-861},
year = {2016},
doi = {10.1021/acssynbio.5b00246},
note = {PMID: 27244532},
url = {http://www.lacl.fr/~michel/PUBLIS/2016/acs2016.pdf},
eprint = {http://dx.doi.org/10.1021/acssynbio.5b00246}
}
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