Christophe Pradal - Academia.edu (original) (raw)
Papers by Christophe Pradal
The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fasc... more The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems Frontiers in Plant Science | www.frontiersin.org 1 June 2017 | Volume 8 | Article 900 Bucksch et al. Plant Morphological Modeling is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fasc... more The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems Frontiers in Plant Science | www.frontiersin.org 1 June 2017 | Volume 8 | Article 900 Bucksch et al. Plant Morphological Modeling is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Comparative Biochemistry and Physiology A-molecular & Integrative Physiology, 2009
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An emerging challenge in plant biology is to develop qualitative and quantitative measures to des... more An emerging challenge in plant biology is to develop qualitative and quantitative measures to describe the appearance of plants through the integration of mathematics and biology. A major hurdle in developing these metrics is finding common terminology across fields. In this review, we define approaches for analyzing plant geometry, topology, and shape, and provide examples for how these terms have been and can be applied to plants. In leaf morphological quantifications both geometry and shape have been used to gain insight into leaf function and evolution. For the analysis of cell growth and expansion, we highlight the utility of geometric descriptors for understanding sepal and hypocotyl development. For branched structures, we describe how topology has been applied to quantify root system architecture to lend insight into root function. Lastly, we discuss the importance of using morphological descriptors in ecology to assess how communities interact, function, and respond within different environments. This review aims to provide a basic description of the mathematical principles underlying morphological quantifications.
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ABSTRACT Unlike trees, the 3D architecture of gramineous plants is much more related to the shape... more ABSTRACT Unlike trees, the 3D architecture of gramineous plants is much more related to the shapes of its leaves than the arrangement of its branches. Many modelling efforts have thus concentrated on correctly capturing its complex shape at different stages and use them as scalable geometric primitives. Still, additional control of such objects is needed in the context of Functional Structural Modelling. The objective of this work is to propose a plastic and dynamic 3D leaf model that is well suited for such uses, still able to capture a variety of observed static shapes. Leaf shape is modeled by a parametric surface describing leaf midrib curvature, leaf width variation, undulation of leaf margins and twist along the midrib. Meshes can be generated from these surfaces, and reduced using a decimation algorithm. The model can be fitted with data or with curves drawn by user interaction. Morphological operators are defined and allows for plastic deformation of the control curves. The dynamics of shape acquisition can also be specified, and combined with morphological operators to simulate various scenarios of evolution and responses to stresses. The capabilities of the model are demonstrated through several cases of use. Future directions of research are thought to be a better integration of mechanical or physiological constraints that would reduce the model plasticity but avoid user-induced unrealistic simulation.
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… and Physiology-Part A: …, Jan 1, 2009
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Résumé This paper presents our recent work on progressive compression of plant models based on ge... more Résumé This paper presents our recent work on progressive compression of plant models based on generalized cylinders. This multi-scale representation is compatible with a direct-acyclic graph representation that allows us to build upon the progressive streaming work of [COM * 07]. We present a method for differential coding of plants : an average branch is computed for any chosen group of branches and then, for each branch, we only need to code a transformation and differences. To be able to stream, we identify and take advantage of two types of dependencies : topological (between mother and daughter branches) and dependencies due to differential coding. We obtain a progressive model that makes it possible to select a lightweight representation of a plant while preserving branch density. Ce papier présente nos travaux récents sur la compression progressive de modèles de plantes à base de cylindres généralisés. Cette représentation multi-resolution est compatible avec une représentat...
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... C. Fournier5, Y. Guédon2, A. Ouangraoua6, C. Smith8, S. Stoma1, F. Théveny2, H. Sinoquet3 and... more ... C. Fournier5, Y. Guédon2, A. Ouangraoua6, C. Smith8, S. Stoma1, F. Théveny2, H. Sinoquet3 and C. Godin1 1 INRIA, 2004 route des lucioles BP 93, 06902 Sophia Antipolis, France 2 ... Pradal C., Boudon F., Donès N., Durand J.-B., Fournier C., Sinoquet H., Godin C. 2006. ...
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IX International Symposium on Modelling in Fruit Research and Orchard Management, 2015
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Proceedings of the 27th International Conference on Scientific and Statistical Database Management - SSDBM '15, 2015
ABSTRACT Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve... more ABSTRACT Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve very complex and inter-linked steps where several tools are combined together. Scientific workflow systems have reached a level of maturity that makes them able to support the design and execution of such in-silico experiments, and thus making them increasingly popular in the bioinformatics community. However, in some emerging application domains such as system biology, developmental biology or ecology, the need for data analysis is combined with the need to model complex multi-scale biological systems, possibly involving multiple simulation steps. This requires the scientific work-flow to deal with retro-action to understand and predict the relationships between structure and function of these complex systems. OpenAlea (openalea.gforge.inria.fr) is the only scientific workflow system able to uniformly address the problem, which made it successful in the scientific community. One of its main originality is to introduce higher-order dataflows as a means to uniformly combine classical data analysis with modeling and simulation. In this demonstration paper, we provide for the first time the description of the OpenAlea system involving an original combination of features. We illustrate the demonstration on a high-throughput workflow in phenotyping, phenomics, and environmental control designed to study the interplay between plant architecture and climatic change.
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2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
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Frontiers in plant science, 2012
The study of plant development requires increasingly powerful modeling tools to help understand a... more The study of plant development requires increasingly powerful modeling tools to help understand and simulate the growth and functioning of plants. In the last decade, the formalism of L-systems has emerged as a major paradigm for modeling plant development. Previous implementations of this formalism were made based on static languages, i.e., languages that require explicit definition of variable types before using them. These languages are often efficient but involve quite a lot of syntactic overhead, thus restricting the flexibility of use for modelers. In this work, we present an adaptation of L-systems to the Python language, a popular and powerful open-license dynamic language. We show that the use of dynamic language properties makes it possible to enhance the development of plant growth models: (i) by keeping a simple syntax while allowing for high-level programming constructs, (ii) by making code execution easy and avoiding compilation overhead, (iii) by allowing a high-level...
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The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fasc... more The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems Frontiers in Plant Science | www.frontiersin.org 1 June 2017 | Volume 8 | Article 900 Bucksch et al. Plant Morphological Modeling is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fasc... more The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems Frontiers in Plant Science | www.frontiersin.org 1 June 2017 | Volume 8 | Article 900 Bucksch et al. Plant Morphological Modeling is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Comparative Biochemistry and Physiology A-molecular & Integrative Physiology, 2009
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An emerging challenge in plant biology is to develop qualitative and quantitative measures to des... more An emerging challenge in plant biology is to develop qualitative and quantitative measures to describe the appearance of plants through the integration of mathematics and biology. A major hurdle in developing these metrics is finding common terminology across fields. In this review, we define approaches for analyzing plant geometry, topology, and shape, and provide examples for how these terms have been and can be applied to plants. In leaf morphological quantifications both geometry and shape have been used to gain insight into leaf function and evolution. For the analysis of cell growth and expansion, we highlight the utility of geometric descriptors for understanding sepal and hypocotyl development. For branched structures, we describe how topology has been applied to quantify root system architecture to lend insight into root function. Lastly, we discuss the importance of using morphological descriptors in ecology to assess how communities interact, function, and respond within different environments. This review aims to provide a basic description of the mathematical principles underlying morphological quantifications.
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ABSTRACT Unlike trees, the 3D architecture of gramineous plants is much more related to the shape... more ABSTRACT Unlike trees, the 3D architecture of gramineous plants is much more related to the shapes of its leaves than the arrangement of its branches. Many modelling efforts have thus concentrated on correctly capturing its complex shape at different stages and use them as scalable geometric primitives. Still, additional control of such objects is needed in the context of Functional Structural Modelling. The objective of this work is to propose a plastic and dynamic 3D leaf model that is well suited for such uses, still able to capture a variety of observed static shapes. Leaf shape is modeled by a parametric surface describing leaf midrib curvature, leaf width variation, undulation of leaf margins and twist along the midrib. Meshes can be generated from these surfaces, and reduced using a decimation algorithm. The model can be fitted with data or with curves drawn by user interaction. Morphological operators are defined and allows for plastic deformation of the control curves. The dynamics of shape acquisition can also be specified, and combined with morphological operators to simulate various scenarios of evolution and responses to stresses. The capabilities of the model are demonstrated through several cases of use. Future directions of research are thought to be a better integration of mechanical or physiological constraints that would reduce the model plasticity but avoid user-induced unrealistic simulation.
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… and Physiology-Part A: …, Jan 1, 2009
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Résumé This paper presents our recent work on progressive compression of plant models based on ge... more Résumé This paper presents our recent work on progressive compression of plant models based on generalized cylinders. This multi-scale representation is compatible with a direct-acyclic graph representation that allows us to build upon the progressive streaming work of [COM * 07]. We present a method for differential coding of plants : an average branch is computed for any chosen group of branches and then, for each branch, we only need to code a transformation and differences. To be able to stream, we identify and take advantage of two types of dependencies : topological (between mother and daughter branches) and dependencies due to differential coding. We obtain a progressive model that makes it possible to select a lightweight representation of a plant while preserving branch density. Ce papier présente nos travaux récents sur la compression progressive de modèles de plantes à base de cylindres généralisés. Cette représentation multi-resolution est compatible avec une représentat...
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... C. Fournier5, Y. Guédon2, A. Ouangraoua6, C. Smith8, S. Stoma1, F. Théveny2, H. Sinoquet3 and... more ... C. Fournier5, Y. Guédon2, A. Ouangraoua6, C. Smith8, S. Stoma1, F. Théveny2, H. Sinoquet3 and C. Godin1 1 INRIA, 2004 route des lucioles BP 93, 06902 Sophia Antipolis, France 2 ... Pradal C., Boudon F., Donès N., Durand J.-B., Fournier C., Sinoquet H., Godin C. 2006. ...
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IX International Symposium on Modelling in Fruit Research and Orchard Management, 2015
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Proceedings of the 27th International Conference on Scientific and Statistical Database Management - SSDBM '15, 2015
ABSTRACT Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve... more ABSTRACT Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve very complex and inter-linked steps where several tools are combined together. Scientific workflow systems have reached a level of maturity that makes them able to support the design and execution of such in-silico experiments, and thus making them increasingly popular in the bioinformatics community. However, in some emerging application domains such as system biology, developmental biology or ecology, the need for data analysis is combined with the need to model complex multi-scale biological systems, possibly involving multiple simulation steps. This requires the scientific work-flow to deal with retro-action to understand and predict the relationships between structure and function of these complex systems. OpenAlea (openalea.gforge.inria.fr) is the only scientific workflow system able to uniformly address the problem, which made it successful in the scientific community. One of its main originality is to introduce higher-order dataflows as a means to uniformly combine classical data analysis with modeling and simulation. In this demonstration paper, we provide for the first time the description of the OpenAlea system involving an original combination of features. We illustrate the demonstration on a high-throughput workflow in phenotyping, phenomics, and environmental control designed to study the interplay between plant architecture and climatic change.
Bookmarks Related papers MentionsView impact
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
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Frontiers in plant science, 2012
The study of plant development requires increasingly powerful modeling tools to help understand a... more The study of plant development requires increasingly powerful modeling tools to help understand and simulate the growth and functioning of plants. In the last decade, the formalism of L-systems has emerged as a major paradigm for modeling plant development. Previous implementations of this formalism were made based on static languages, i.e., languages that require explicit definition of variable types before using them. These languages are often efficient but involve quite a lot of syntactic overhead, thus restricting the flexibility of use for modelers. In this work, we present an adaptation of L-systems to the Python language, a popular and powerful open-license dynamic language. We show that the use of dynamic language properties makes it possible to enhance the development of plant growth models: (i) by keeping a simple syntax while allowing for high-level programming constructs, (ii) by making code execution easy and avoiding compilation overhead, (iii) by allowing a high-level...
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