Jerome Chopard

Post-doctoral research fellow

Phto

 

Provenance of scientific workflows computed on the grid.

Phenome project, INRA LEPSE – MISTEA

  • Tel: 04 67 14 97 89
  • Email: jerome.chopard@inria.fr

Selected publications

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Publications HAL de jerome, chopard

2017

Journal articles

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Christophe Pradal, Simon Artzet, Jerome Chopard, Dimitri Dupuis, Christian Fournier, et al.. InfraPhenoGrid: A scientific workflow infrastructure for Plant Phenomics on the Grid. Future Generation Computer Systems, Elsevier, 2017, 67, pp.341-353. 〈10.1016/j.future.2016.06.002〉. 〈hal-01336655〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01336655/file/infraphenogrid-scientific-workflow_pradal16.pdf BibTex
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Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, et al.. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, Elsevier, 2017, 〈10.1016/j.future.2017.01.012〉. 〈hal-01516082〉
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01516082/file/Cohen-Boulakia-etal-reproductibility.pdf BibTex

2016

Conference papers

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Simon Artzet, Nicolas Brichet, Llorenc Cabrera, Tsu-Wei Chen, Jerome Chopard, et al.. Image workflows for high throughput phenotyping platforms. BMVA technical meeting: Plants in Computer Vision, Nov 2016, London, United Kingdom. 〈https://www.eventbrite.co.uk/e/bmva-technical-meeting-plants-in-computer-vision-registration-24677394752#〉. 〈hal-01459040〉
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Tsu-Wei Chen, Christian Fournier, Simon Artzet, Nicolas Brichet, Jérôme Chopard, et al.. Genetic variability in light-related parameters of maize models revealed by linking 3D-reconstruction of plant architecture with light model and phenotyping platform. 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), Nov 2016, Qingdao, China. 2016 IEEE International Conference on Functional-Structural Plant Growth Modeling, Simulation, Visualization and Applications (FSPMA 2016), 〈www.fspma.net〉. 〈hal-01396935〉
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2015

Journal articles

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Frédéric Boudon, Jérôme Chopard, Olivier Ali, Benjamin Gilles, Olivier Hamant, et al.. A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution. PLoS Computational Biology, Public Library of Science, 2015, 11 (1), pp.1-16. 〈10.1371/journal.pcbi.1003950〉. 〈hal-01142486〉
Accès au texte intégral et bibtex
https://hal.archives-ouvertes.fr/hal-01142486/file/boudon-plos-compbiol15.pdf BibTex

Poster communications

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Christian Fournier, Simon Artzet, Jérôme Chopard, Michael Mielewczik, Nicolas Brichet, et al.. Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data. IAMPS 2015 (International Workshop on Image Analysis Methods for the Plant Sciences), Sep 2015, Louvain-la-Neuve, Belgium. 〈http://www.phytosystems.ulg.ac.be/iamps15/〉. 〈hal-01253627〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-01253627/file/Phenomenal%40IAMPS.pdf BibTex

2014

Journal articles

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Daniele Muraro, Nathan Mellor, Michael P. Pound, Hanna Help, Mikaël Lucas, et al.. Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2014, 111 (2), pp.857-862. 〈10.1073/pnas.1221766111〉. 〈hal-00941028〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00941028/file/Muraro14.pdf BibTex

2011

Journal articles

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Camillo La Rota, Jérôme Chopard, Pradeep Das, Sandrine Paindavoine, Frédérique Rozier, et al.. A data-driven integrative model of sepal primordium polarity in Arabidopsis. The Plant cell, American Society of Plant Biologists (ASPB), 2011, 23 (12), pp.4318-433. 〈10.1105/tpc.111.092619〉. 〈hal-00828854〉
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Conference papers

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Jérôme Chopard, Christophe Pradal, Daniel Barbeau, Thomas Cokelaer, Christophe Godin. Scientific workflow for reusing plant/FSPM models. Chan, F. and Marinova, D. and Anderssen, R.S. MODSIM2011. 19th International Congress on Modelling and Simulation, Dec 2011, Perth, Australia. pp.968-974, 2011, MODSIM2011. 19th International Congress on Modelling and Simulation. 〈hal-00790635〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00790635/file/MODSIM11_openalea.pdf BibTex

2010

Journal articles

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Francine Perrine-Walker, Patrick Doumas, Mikael Lucas, Virginie Vaissayre, Nicholas J Beauchemin, et al.. Auxin carriers localization drives auxin accumulation in plant cells infected by Frankia in Casuarina glauca actinorhizal nodules.. Plant Physiology, American Society of Plant Biologists, 2010, 154 (3), pp.1372-80. 〈10.1104/pp.110.163394〉. 〈hal-00554754〉
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Conference papers

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Jérôme Chopard, Christophe Godin. The role of mechanics in morphogenesis. DeJong, Theodore and Da Silva, David. 6th International Workshop on Functional-Structural Plant Models, 2010, Davis, CA, United States. pp.135-137, 2010. 〈hal-00831791〉
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ref_biblio
Christophe Pradal, Thomas Cokelaer, Daniel Barbeau, Eric Moscardi, Jérôme Chopard, et al.. Modeling Strategies Using Visual Programming in OpenAlea. DeJong, Theodore and Da Silva, David. 6th International Workshop on Functional-Structural Plant Models, 2010, Davis, CA, United States. pp.101-103, 2010. 〈hal-00831785〉
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2009

Journal articles

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Christophe Pradal, Frédéric Boudon, Christophe Nouguier, Jérôme Chopard, Christophe Godin. PlantGL: A Python-based geometric library for 3D plant modelling at different scales. Graphical Models, Elsevier, 2009, 71 (1), 1–21, posted-at = 2008-11-04 14:10:07. 〈10.1016/j.gmod.2008.10.001〉. 〈hal-00850782〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00850782/file/plantgl.pdf BibTex

2008

Journal articles

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Claude-Eric Parveaud, Jérome Chopard, Jean Dauzat, Benoît Courbaud, Daniel Auclair. Modelling foliage characteristics in 3D tree crowns: influence on light interception and leaf irradiance. Trees – Structure and Function, Springer Verlag, 2008, 22 (1), pp.87-104. 〈10.1007/s00468-007-0172-9〉. 〈halsde-00258970〉
Accès au bibtex
BibTex
ref_biblio
Szymon Stoma, M. Lucas, Jérôme Chopard, Marianne Schaedel, Jan Traas, et al.. Flux based transport enhancement as a plausible unifying mechanism for Auxin transport in meristem development. PLoS Computational Biology, Public Library of Science, 2008, 4 (10), pp.1000207. 〈10.1371/journal.pcbi.1000207〉. 〈hal-00412857〉
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2007

Conference papers

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Samuel Dufour-Kowalski, Christophe Pradal, Nicolas Dones, Pierre Barbier de Reuille, Frédéric Boudon, et al.. OpenAlea: An open-source platform for the integration of heterogeneous FSPM components. FSPM07 – 5th International Workshop on Functional-Structural Plant Models, Nov 2007, Napier, New Zealand. pp.P36:1-2, 2007. 〈hal-00831824〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00831824/file/openalea-abstractfspm.pdf BibTex
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Szymon Stoma, Jérôme Chopard, Christophe Godin, Jan Traas. Using mechanics in the modelling of meristem morphogenesis. 5th International Workshop on Functional-Structural Plant Models, 2007, Napier, New Zealand. pp.52, 1–4, 2007. 〈hal-00831832〉
Accès au texte intégral et bibtex
https://hal.inria.fr/hal-00831832/file/stomafspm.pdf BibTex
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Jérôme Chopard, Christophe Godin, Jan Traas. Towards a formal expression of morphogenesis: a mechanics based integration of cell growth at tissue scale. Crook, Nigel and olde Scheper, Tjeerd. Proceedings of the 7th International Workshop on Information Processing in Cells and Tissues, 2007, Oxford, United Kingdom. librix.eu, pp.387-399, 2007. 〈hal-00831831〉
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Directions of work or proceedings

ref_biblio
Samuel Dufour-Kowalski, Christophoe Pradal, Nicolas Dones, Pierre Barbier de Reuille, Frédéric Boudon, et al.. OpenAlea: an open-source platform for the integration of heterogeneous FSPM components. 5. International Workshop on Functional-Structural Plant Models, 2007, Napier, New Zealand. pp.36, 2007. 〈hal-01189279〉
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Reports

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Christophe Pradal, Frédéric Boudon, Christophe Nouguier, Jérôme Chopard, Christophe Godin. PlantGL : a Python-based geometric library for 3D plant modelling at different scales. [Research Report] RR-6367, INRIA. 2007. 〈inria-00191126v3〉
Accès au texte intégral et bibtex
https://hal.inria.fr/inria-00191126/file/RR-6367.pdf BibTex

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