Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Ricardo Honorato-Zimmer"'
Publikováno v:
Logical Methods in Computer Science, Vol Volume 11, Issue 2 (2015)
We develop a new thermodynamic approach to stochastic graph-rewriting. The ingredients are a finite set of reversible graph-rewriting rules called generating rules, a finite set of connected graphs P called energy patterns and an energy cost function
Externí odkaz:
https://doaj.org/article/80f5b439a32f4048b0d707cfa6c24b74
Publikováno v:
CMSB 2020-18th International Conference Computational Methods in Systems Biology
CMSB 2020-18th International Conference Computational Methods in Systems Biology, Sep 2020, Konstanz / Virtual, Germany. pp.3-26, ⟨10.1007/978-3-030-60327-4_1⟩
Computational Methods in Systems Biology ISBN: 9783030603267
CMSB
CMSB 2020-18th International Conference Computational Methods in Systems Biology, Sep 2020, Konstanz / Virtual, Germany. pp.3-26, ⟨10.1007/978-3-030-60327-4_1⟩
Computational Methods in Systems Biology ISBN: 9783030603267
CMSB
In this paper, we combine ideas from two different scientific traditions: 1) graph transformation systems (GTSs) stemming from the theory of formal languages and concurrency, and 2) mean field approximations (MFAs), a collection of approximation tech
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5b37bd90b819371c8f5ea7293fa26bd4
https://hal.science/hal-03096240/file/2008.11066.pdf
https://hal.science/hal-03096240/file/2008.11066.pdf
Publikováno v:
SASB
University of Edinburgh-PURE
Honorato Zimmer, R, Millar, A, Plotkin, G & Zardilis, A 2016, Chromar, a rule-based language of parameterised objects . in The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016) . The Seventh International Workshop on Static Analysis and Systems Biology, Edinburgh, United Kingdom, 7/09/16 .
Honorato-Zimmer, R, Millar, A J, Plotkin, G D & Zardilis, A 2018, ' Chromar, a Rule-based Language of Parameterised Objects ', Electronic Notes in Theoretical Computer Science, vol. 335, pp. 49-66 . https://doi.org/10.1016/j.entcs.2018.03.008
University of Edinburgh-PURE
Honorato Zimmer, R, Millar, A, Plotkin, G & Zardilis, A 2016, Chromar, a rule-based language of parameterised objects . in The Seventh International Workshop on Static Analysis and Systems Biology (SASB 2016) . The Seventh International Workshop on Static Analysis and Systems Biology, Edinburgh, United Kingdom, 7/09/16 .
Honorato-Zimmer, R, Millar, A J, Plotkin, G D & Zardilis, A 2018, ' Chromar, a Rule-based Language of Parameterised Objects ', Electronic Notes in Theoretical Computer Science, vol. 335, pp. 49-66 . https://doi.org/10.1016/j.entcs.2018.03.008
Modelling in biology becomes necessary when systems are complex but the more complex the systems are the harder the models become to read. The most common ways of writing models are by writing reactions on discrete, typed objects (e.g. molecules of d
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0f390eded96634c64b0ef2b91ae398f9
https://doi.org/10.1016/j.entcs.2018.03.008
https://doi.org/10.1016/j.entcs.2018.03.008
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 1945
The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated g
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::8e73460306fd190de259f8dbf9f3c6e1
https://pubmed.ncbi.nlm.nih.gov/30945252
https://pubmed.ncbi.nlm.nih.gov/30945252
Publikováno v:
Modeling Biomolecular Site Dynamics ISBN: 9781493991006
The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated g
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::58b20fc2956355c54af1f2439f65d296
https://doi.org/10.1007/978-1-4939-9102-0_13
https://doi.org/10.1007/978-1-4939-9102-0_13
Autor:
Ricardo Honorato-Zimmer
Publikováno v:
Ricardo Honorato-Zimmer
We explore the direct and inverse problem of thermodynamics in the context of rule-based modelling. The direct problem can be concisely stated as obtaining a set of rewriting rules and their rates from the description of the energy landscape such tha
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::1980b96d92192025ab08cc99ae94827e
http://hdl.handle.net/1842/28904
http://hdl.handle.net/1842/28904
Autor:
Vincent Danos, Ricardo Honorato-Zimmer
Publikováno v:
2016 IEEE 1st International Workshops on Foundations and Applications of Self* Systems (FAS*W)
2016 IEEE 1st International Workshops on Foundations and Applications of Self* Systems (FAS*W), Sep 2016, Augsburg, Germany. pp.24-29
Danos, V & Honorato Zimmer, R 2016, Emergent Communities in Socio-Cognitive Networks . in IEEE International Workshops on Foundations and Applications of Self* Systems . Institute of Electrical and Electronics Engineers (IEEE), Augsburg, Germany, pp. 24-29, 2016 IEEE 1st International Workshops on Foundations and Applications of Self* Systems, Augsburg, Germany, 12/09/16 . https://doi.org/10.1109/FAS-W.2016.19
FAS*W@SASO/ICCAC
2016 IEEE 1st International Workshops on Foundations and Applications of Self* Systems (FAS*W), Sep 2016, Augsburg, Germany. pp.24-29
Danos, V & Honorato Zimmer, R 2016, Emergent Communities in Socio-Cognitive Networks . in IEEE International Workshops on Foundations and Applications of Self* Systems . Institute of Electrical and Electronics Engineers (IEEE), Augsburg, Germany, pp. 24-29, 2016 IEEE 1st International Workshops on Foundations and Applications of Self* Systems, Augsburg, Germany, 12/09/16 . https://doi.org/10.1109/FAS-W.2016.19
FAS*W@SASO/ICCAC
International audience; We investigate a recent network model [13] which combines social and cognitive features. Each node in the social network holds a (possibly different) cognitive network that represent its beliefs. In this internal cognitive net
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60ab1dce6a464750502cf54230eb1d82
https://hal.archives-ouvertes.fr/hal-01976443
https://hal.archives-ouvertes.fr/hal-01976443
Autor:
Owen Gilfellon, Curtis Madsen, Goksel Misirli, Matteo Cavaliere, Paolo Zuliani, Anil Wipat, Matthew Pocock, Vincent Danos, William Waites, Ricardo Honorato-Zimmer
Publikováno v:
Bioinformatics
Bioinformatics, 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Misirli, G, Cavaliere, M, Waites, W, Pocock, M, Madsen, C, Gilfellon, O, Honorato Zimmer, R, Zuliani, P, Danos, V & Wipat, A 2016, ' Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation ', Bioinformatics, vol. 32, no. 6, pp. 908-917 . https://doi.org/10.1093/bioinformatics/btv660
Bioinformatics, 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2015, ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, Oxford University Press (OUP), 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Bioinformatics, 2016, 32 (6), pp.908-917. ⟨10.1093/bioinformatics/btv660⟩
Misirli, G, Cavaliere, M, Waites, W, Pocock, M, Madsen, C, Gilfellon, O, Honorato Zimmer, R, Zuliani, P, Danos, V & Wipat, A 2016, ' Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation ', Bioinformatics, vol. 32, no. 6, pp. 908-917 . https://doi.org/10.1093/bioinformatics/btv660
International audience; Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation. Bioinformatics 2015, ABSTRACT Motivation: Biological systems are complex and challenging to model and therefore model
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e161d8efa0ea476c286e5a20d557de46
https://hal.science/hal-01263639
https://hal.science/hal-01263639
Publikováno v:
Electronic Notes in Theoretical Computer Science
Electronic Notes in Theoretical Computer Science, Elsevier, 2015, 313, pp.47-64. ⟨10.1016/j.entcs.2015.04.018⟩
Danos, V, Honorato Zimmer, R, Jaramillo-Riveri, S & Stucki, S 2015, ' Coarse-graining the Dynamics of Ideal Branched Polymers ', Electronic Notes in Theoretical Computer Science, vol. 313, pp. 47-64 . https://doi.org/10.1016/j.entcs.2015.04.018
Electronic Notes in Theoretical Computer Science, 2015, 313, pp.47-64. ⟨10.1016/j.entcs.2015.04.018⟩
Electronic Notes in Theoretical Computer Science, Elsevier, 2015, 313, pp.47-64. ⟨10.1016/j.entcs.2015.04.018⟩
Danos, V, Honorato Zimmer, R, Jaramillo-Riveri, S & Stucki, S 2015, ' Coarse-graining the Dynamics of Ideal Branched Polymers ', Electronic Notes in Theoretical Computer Science, vol. 313, pp. 47-64 . https://doi.org/10.1016/j.entcs.2015.04.018
Electronic Notes in Theoretical Computer Science, 2015, 313, pp.47-64. ⟨10.1016/j.entcs.2015.04.018⟩
International audience; We define a class of local stochastic rewrite rules on directed site trees. We give a compact presentation of (often countably infinite) coarse-grained differential systems describing the dynamics of these rules in the determi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::eeb7dfe8e685a3d248ad2161a5ea16a6
https://hal.archives-ouvertes.fr/hal-01976312/file/Coarse-graining_1-s2.0-S1571066115000225-main.pdf
https://hal.archives-ouvertes.fr/hal-01976312/file/Coarse-graining_1-s2.0-S1571066115000225-main.pdf
Publikováno v:
Reversible Computation ISBN: 9783319208596
RC
LNCS
7th International Conference, Reversible Computation 2015
7th International Conference, Reversible Computation 2015, Jul 2015, Grenoble, France. pp.3-26, ⟨10.1007/978-3-319-20860-2_1⟩
Danos, V, Heindel, T, Honorato-zimmer, R & Stucki, S 2015, Moment Semantics for Reversible Rule-Based Systems . in Reversible Computation : 7th International Conference, RC 2015, Grenoble, France, July 16-17, 2015, Proceedings ., Chapter 1, Lecture Notes in Computer Science, vol. 9138, pp. 3-26 . https://doi.org/10.1007/978-3-319-20860-2_1
RC
LNCS
7th International Conference, Reversible Computation 2015
7th International Conference, Reversible Computation 2015, Jul 2015, Grenoble, France. pp.3-26, ⟨10.1007/978-3-319-20860-2_1⟩
Danos, V, Heindel, T, Honorato-zimmer, R & Stucki, S 2015, Moment Semantics for Reversible Rule-Based Systems . in Reversible Computation : 7th International Conference, RC 2015, Grenoble, France, July 16-17, 2015, Proceedings ., Chapter 1, Lecture Notes in Computer Science, vol. 9138, pp. 3-26 . https://doi.org/10.1007/978-3-319-20860-2_1
International audience; We develop a notion of stochastic rewriting over marked graphs – i.e. directed multigraphs with degree constraints. The approach is based on double-pushout (DPO) graph rewriting. Marked graphs are expressive enough to intern
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a3c2cf7d0c399f132028af4f93ff322b
https://doi.org/10.1007/978-3-319-20860-2_1
https://doi.org/10.1007/978-3-319-20860-2_1