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1. Open Data for Environment Sensing: Crowdsourcing Geolocation Data

Author

Ngoan Trieu, Zachary Williams, Jean-François Dorville, Hiep Huynh, Vincent Rodin, and Bernard Pottier

Subjects
open data, web semantic, environment sensing, geolocation data, and environmental simulation, Technology (General), T1-995
Abstract

There are numerous situations where the digital representation of the environment appears critical for understanding and decision-making: threats on soils, water, seashores, risk of fires, pollutions are evident applications. If spatial cellular decomposition is evidence in the more common applications, there remains a large field for environment and activities modelling. The integration and composition of several information sources is perhaps the main difficulty with the need to deal with data interpretation and semantics inside concurrent simulators. Besides, the data on population, people's behaviours, people's perceptions are essential in environmental assessments, where the technical aspect is not counted as much as the common acceptance of impact technology. We provide a model for building environmental services with open data systems. A case study is given for getting information from the public about their relationship with freshwater and its scarcity in Jamaica.

Published
2020
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2. Évaluation et optimisation des algorithmes de restauration d'images sous-marines

Author

Hai Nam Tran, Vincent Rodin, Barbara Dzaja, Artur Mkrtchyan, Alan Le Boudec, Université de Brest (UBO), Laboratoire des Sciences et des Technologies de l'Information et de la Communication (LabSTIC), Université 08 mai 45 Guelma [Algérie], Yerevan State University, and MKRTCHYAN, Artur

Subjects
Computer science, Image quality, media_common.quotation_subject, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Cognitive neuroscience of visual object recognition, 020206 networking & telecommunications, [INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS], 02 engineering and technology, image restauration, underwater, ROV, Drone, Image (mathematics), [INFO.INFO-ES] Computer Science [cs]/Embedded Systems, Underwater vehicle, [INFO.INFO-TI] Computer Science [cs]/Image Processing [eess.IV], [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Quality (business), [INFO.INFO-ES]Computer Science [cs]/Embedded Systems, 14. Life underwater, Underwater, Algorithm, Image restoration, media_common
Abstract

On-board restoration of underwater images on embedded platforms such as marine drones is faced with many obstacles including image quality and real-time constraints. Confrontations met on the way vary from views to solution methods depending on the goals, such as underwater vehicle realtime control and positioning or underwater object recognition. In this research, five algorithms for underwater image restoration were studied and evaluated. In order to evaluate the quality of the performing algorithms nine evaluation criteria were used. Split into two types, the no reference metrics assesses only the quality of the image results, while the full reference criterion uses a reference image to estimate it. The calculation of these criteria allows each algorithm to be compared. Furthermore, the possibility to optimise algorithms in order to make them applicable to meet real-time requirements on embedded platforms was investigated., La restauration embarquée d'images sous-marines sur des plates-formes embarquées telles que les drones marins est confrontée à de nombreux obstacles dont la qualité des images et les contraintes de temps réel. Les confrontations rencontrées en cours de route varient des points de vue aux méthodes de solution en fonction des objectifs, tels que le contrôle et le positionnement en temps réel du véhicule sous-marin ou la reconnaissance d'objets sous-marins. Dans cette recherche, cinq algorithmes de restauration d'images sous-marines ont été étudiés et évalués. Afin d'évaluer la qualité des algorithmes performants, neuf critères d'évaluation ont été utilisés. Divisés en deux types, le critère sans référence évalue uniquement la qualité des résultats de l'image, tandis que le critère avec référence complète utilise une image de référence pour l'estimer. Le calcul de ces critères permet de comparer chaque algorithme. En outre, la possibilité d'optimiser les algorithmes afin de les rendre applicables pour répondre aux exigences du temps réel sur les plateformes embarquées a été étudiée.

Published
2021

3. An Interruptible Task Allocation Model : Application to a Honey Bee Colony Simulation

Author

Cédric Alaux, Yves Le Conte, Frank Singhoff, Thierry Duval, Thomas Alves, Jérémy Rivière, Vincent Rodin, Lab-STICC_UBO_CID_IHSEV, Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Institut Mines-Télécom [Paris] (IMT)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-Institut Mines-Télécom [Paris] (IMT)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL), Abeilles et Environnement (AE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Equipe Software/HArdware and unKnown Environment inteRactions (Lab-STICC_SHAKER), Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL), Lab-STICC_IMTA_CID_IHSEV, Département Informatique (IMT Atlantique - INFO), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Yves Demazeau, Tom Holvoet, Juan Manuel Corchado, and and Stefania Costantini

Subjects
[INFO.INFO-CC]Computer Science [cs]/Computational Complexity [cs.CC], 0303 health sciences, business.industry, Computer science, Swarm robotics, Honey bee, Stimulus (physiology), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], 03 medical and health sciences, Honey Bees, 0302 clinical medicine, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Intrinsic motivation, Artificial intelligence, Interrupt, Threshold model, business, 030217 neurology & neurosurgery, Division of labour, 030304 developmental biology
Abstract

International audience; Division of labour is a key aspect of distributed systems, such as swarm robotics or multi-agent systems. Inspired by social insects known for their task allocation capabilities, most of the models rely on two assumptions: 1) each task is associated with a stimulus, and 2) the execution of this task lowers that stimulus. In short, the stimulus is a representation of the amount of work needed on a task. When these assumptions are not true, we need a mechanism to guide the agent in its decision whether to pursue or to interrupt its current task, as there is no diminishing stimulus to rely on. In this article, we propose a model based on the Response Threshold Model and a mechanism based on the agent’s intrinsic motivation and internal states, allowing to take into account tasks dissociated from stimuli. Agents use their intrinsic motivation to emulate the priority of tasks not associated with any stimuli, and to decide whether to interrupt or pursue their current task. This model has been applied to simulate the division of labour within a simplified honey bee colony, associated with the constantly adapting physiology of honey bees. Preliminary results show that the task allocation is effective, robust and in some cases improved by the interruption mechanism.

Published
2020

4. Viability Kernel Algorithm for Shapes Equilibrium

Author

Alexandra Fronville, Vincent Rodin, and Abdoulaye Sarr

Subjects
computational modeling, mutational analysis, Mathematical optimization, epigenetics, Differential equation, lcsh:R, hybrid automata, lcsh:Medicine, Time horizon, General Medicine, Biology, Topology, Engineered tissues, Constraint (information theory), State space, Initial value problem, Hybrid automaton, Uniqueness, Limit (mathematics), viability theory
Abstract

Viability is a very important feature of dynamic systems under state constraints whose initial value problem does not ensure uniqueness of solutions. In this paper, we introduce an hybrid automaton to address the question of viability of a cellular tissue. This hybrid automaton couples two dynamical models: differential equations manage the energy of the system and morphological equations govern the growth of the tissue. The cells can proliferate when they have enough access to oxygen and nutrient to produce the energy, remain quiescent when this energy is between two levels, or die when this energy is too low. The constraint we choose is to maintain the number of cells of the tissue during a certain time horizon. We have shown that for all the 1029 2D-tissues of 16 cells with an associate genotype, only 5 are viable for this constraint in a long time horizon. Moreover, for all these tissues, they renew there cells periodically. These periodic shapes are like periodic limit cycles in the state space of shapes.

Published
2017

5. Immersive and interactive visualisation of a virtual honey bee colony

Author

Thierry Duval, Jérémy Rivière, Vincent Rodin, Thomas Alves, Lab-STICC_UBO_CID_IHSEV, Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), Institut Mines-Télécom [Paris] (IMT)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-Institut Mines-Télécom [Paris] (IMT)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL), Université de Brest (UBO), Département Logique des Usages, Sciences sociales et Sciences de l'Information (IMT Atlantique - LUSSI), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Lab-STICC_IMTA_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), and Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)

Subjects
Computer science, 05 social sciences, Control (management), GRASP, Frame (networking), 020207 software engineering, 02 engineering and technology, Plan (drawing), Honey bee, Work in process, [INFO.INFO-GR]Computer Science [cs]/Graphics [cs.GR], Task (project management), Human–computer interaction, 0202 electrical engineering, electronic engineering, information engineering, 0501 psychology and cognitive sciences, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], Interactive visualization, 050107 human factors
Abstract

International audience; Social insects and more specifically honey bees have very complex, powerful and interesting task allocation abilities. They are able to distribute their workforce effectively without any central control, using simple mechanisms based on stimuli (dances, pheromones), interactions, thresholds and feedback loops. Self-organisational concepts and some of those mechanisms, like pheromones, are invisible to the human eye. In order to help the user grasp the complexity of the task allocation, we propose to make them visible in a virtual, immersive and interactive environment. First, this implies that the system must be able to simulate and display in real-time around 30 000 bees interacting with each other, emitting clouds of pheromones. Secondly, this implies also that the user should be able to alter in real-time the environment of the bees (e.g. by manipulating the frame of the hive) and visualise the effects on the organisation, potentially days later. Finally, we would like to give to biologists and beekeepers some domain-related, intuitive and natural ways of interacting with the hive. We describe in this article these issues in more details, and how we plan to tackle them. This is a "work in progress", therefore a lot of work has still to be done, mostly surveying and modelling the interactions.

Published
2019
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6. 3D individual based model for simultaneous growth and interaction of L. Monocytogenes and lactic acid bacteria

Author

Gireg Desmeulles, Fabrice Harrouet, Dominique Thuault, Véronique Huchet, Pascal Redou, Laurent Gaubert, Guillaume Longelin Péron, Pascal Ballet, Vincent Rodin, Lab-STICC_ENIB_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), ADRIA Développement, Laboratoire de Traitement de l'Information Medicale (LaTIM), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Mines-Télécom [Paris] (IMT), Lab-STICC_UBO_CID_IHSEV, and Harrouet, Fabrice

Subjects
food and beverages, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
Abstract

International audience; By interacting with pathogens, lactic acid bacteria (LAB) are able to contribute to food safety. By means of their lactic acid production which induces pH decrease, LAB influence the growth of pathogens. The aim of this study is to model and simulate lactic acid production, pH evolution, according to carbohydrate concentration in media, temperature, water activity and ratio of both population.

Published
2015

7. A Multiagent System for Edge Detection and Continuity Perception on Fish Otolith Images

Author

Herve Troadec, Vincent Rodin, Abdesslam Benzinou, Anne Guillaud, and Jean Le Bihan

Subjects
0106 biological sciences, Computer science, media_common.quotation_subject, lcsh:TK7800-8360, 02 engineering and technology, 01 natural sciences, Edge detection, Task (project management), otolith, lcsh:Telecommunication, Perception, lcsh:TK5101-6720, 0202 electrical engineering, electronic engineering, information engineering, medicine, Computer vision, Electrical and Electronic Engineering, Otolith, media_common, edge detection, Ring (mathematics), business.industry, 010604 marine biology & hydrobiology, multiagent system, lcsh:Electronics, Identification (information), medicine.anatomical_structure, Hardware and Architecture, Signal Processing, %22">Fish , 020201 artificial intelligence & image processing, Artificial intelligence, business
Abstract

We present an algorithm for fish otolith growth ring detection using a multiagent system. Up to now, the identification of growth rings, for age estimation, is routinely achieved by human readers, but this task is tedious and depends on the reader subjectivity. One of the major problems encountered during an automatic contour detection is the lack of ring continuity perception. We present an approach to improve this continuity perception based on a 2D reconstruction of rings using a multiagent system. The originality of the approach is to use local edge detection achieved by agents and combine it with continuity perception that active contours allow.

Published
2002

8. French Flag Tracking by Morphogenetic Simulation Under Developmental Constraints

Author

Alexandra Fronville, Vincent Rodin, Abdoulaye Sarr, Pascal Ballet, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), and Springer International Publishing

Subjects
Cognitive science, 0303 health sciences, Mathematical modelling, Process (engineering), Multi-agent system, 02 engineering and technology, Biology, Base (topology), Genome, French flag problem, 03 medical and health sciences, Simulation of biological systems, 0202 electrical engineering, electronic engineering, information engineering, Key (cryptography), Morphogenesis, 020201 artificial intelligence & image processing, Cellular dynamics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Simulation, 030304 developmental biology, Flag (geometry)
Abstract

International audience; Below the influence of the mechanical cues and genetic expression, constraints underlying the developmental process play a key role in forms’ emergence. Theses constraints lead to cells’ differentiation and sometimes determine the directions of cells growth. To better understand these phenomena, we present in this paper our work focused primarily on a development of a mathematical model. A one which takes into account the co-evolution of cellular dynamics with it’s environment. To study the influence of the developmental constraints, we have developed algorithms to make and explore a base of genomes. The purpose of this exploration is first to check conditions under which specific genes are activated. Then, this exploration allows us to follow the conditions of emergence of some patterns that lead to a specific shape. From our model, we found a genome that can generate the French flag. With this French flag pattern and its genome starting, we addressed the following question: is there another genome in the simulated base that achieves the same shape, i.e. the French flag pattern?

Published
2014

9. An Efficient Biomechanical Cell Model to Simulate Large Multi-cellular Tissue Morphogenesis: Application to Cell Sorting Simulation on GPU

Author

Vincent Rodin, Anne Jeannin-Girardon, Pascal Ballet, Lab-STICC_TB_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Région Bretagne, Springer, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance ( Lab-STICC ), École Nationale d'Ingénieurs de Brest ( ENIB ) -Université de Bretagne Sud ( UBS ) -Université de Brest ( UBO ) -Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques ( IBNM ), Université de Brest ( UBO ) -Université européenne de Bretagne ( UEB ) -ENSTA Bretagne-Institut Mines-Télécom [Paris]-Centre National de la Recherche Scientifique ( CNRS ) -École Nationale d'Ingénieurs de Brest ( ENIB ) -Université de Bretagne Sud ( UBS ) -Université de Brest ( UBO ) -Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques ( IBNM ), and Université de Brest ( UBO ) -Université européenne de Bretagne ( UEB ) -ENSTA Bretagne-Institut Mines-Télécom [Paris]-Centre National de la Recherche Scientifique ( CNRS )

Subjects
J.3, Scale (ratio), Computer science, Spring system, Context (language use), Parallel computing, High-performance simulation, 01 natural sciences, Multi-Agent Systems, 03 medical and health sciences, 0103 physical sciences, Synchronization (computer science), Tissue morphogenesis, Graphics, 010306 general physics, Simulation, 030304 developmental biology, ComputingMethodologies_COMPUTERGRAPHICS, 0303 health sciences, OpenCL, Multi-agent system, Cell model, Virtual cell, Cell sorting, Virtual biology, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], [ INFO.INFO-MA ] Computer Science [cs]/Multiagent Systems [cs.MA]
Abstract

International audience; In the context of tissue morphogenesis study, in silico simulations can be seen as experiments in a virtual lab bench. Such simulations can facilitate the comprehension of a system, the test of hypotheses or the incremental refining of a model and its parameters. In silico simulations must be efficient and provide the possibility to simulate large tissues, containing thousands of cells. We propose to study tissue morphogenesis at the cellular level using our virtual biomechanical cell model. This model is based on a mass/spring system and coupled to a multi-agent system. We validated the relevance of our model through a case study: a cell sorting. Moreover, we took advantage of the large parallelism offered by graphics processing units (GPU), which contain up to thousands of cores: we implemented our model with the OpenCL framework. We ran large scale simulations, with up to 106 of our virtual cells. We studied the performance of our system on a CPU Intel Core i7 860, and two GPUs: a NVidia GeForce GT440 and a Nvidia GeForce GTX 690. The absence of synchronization in our implementation allowed the full benefits of the parallelism of these hardwares.

Published
2013

10. In silico study of mechanical stresses at the cellular level during tissue development

Author

Vincent Rodin, Pascal Ballet, Anne Jeannin-Girardon, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), and Région Bretagne

Subjects
0303 health sciences, J.3, In silico, Cell, Morphogenesis, Motility, Biology, Cellular level, Cell biology, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], medicine, Biological cell, Mechanotransduction, Mitosis, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

4 pages; International audience; Mechanical contraints play a key role in tissue morphogenesis. We propose to study these mechanisms at the cellular level, thanks to our virtual biomechanical cell model. This model defines biological cell behaviors, such as cell motility, mitosis and adhesion as well as methods to evaluate cell compression/stretching and shearing. The evaluation of these constraints allows the virtual cells to respond by changing their color during simulation and lead to the observation of emerging patterns in cell differentiation during tissue growth: the main purpose of this evaluation is to give the cells the ability to respond to mechanical constraints by differentiating. This approach allows to study the influence of mechanotransduction during tissue morphogenesis.

Published
2013

11. A Software Architecture for Multi-Cellular System Simulations on Graphics Processing Units

Author

Anne Jeannin-Girardon, Pascal Ballet, Vincent Rodin, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), and Région Bretagne

Subjects
J.3, Computer science, 0206 medical engineering, GPU, 02 engineering and technology, computer.software_genre, Models, Biological, General Biochemistry, Genetics and Molecular Biology, Database-centric architecture, Computational science, 03 medical and health sciences, CUDA, Computer Graphics, Reference architecture, Graphics, 030304 developmental biology, General Environmental Science, 0303 health sciences, OpenCL, business.industry, Applied Mathematics, General Medicine, Modular design, Virtual biology, Multi-cellular systems, Parallel architecture, Philosophy, Computer architecture, Virtual machine, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], General-purpose computing on graphics processing units, General Agricultural and Biological Sciences, Software architecture, business, computer, Software, 020602 bioinformatics, Simulation
Abstract

10 pages; International audience; The first aim of simulation in virtual environment is to help biologists to have a better understanding of the simulated system. The cost of such simulation is significantly reduced compared to that of in vivo simulation. However, the inherent complexity of biological system makes it hard to simulate these systems on non-parallel architectures: models might be made of sub-models and take several scales into account; the number of simulated entities may be quite large. Today, graphics cards are used for general purpose computing which has been made easier thanks to frameworks like CUDA or OpenCL. Parallelization of models may however not be easy: parallel computer programing skills are often required; several hardware architectures may be used to execute models. In this paper, we present the software architecture we built in order to implement various models able to simulate multi-cellular system. This architecture is modular and it implements data structures adapted for graphics processing units architectures. It allows efficient simulation of biological mechanisms.

Published
2013

12. Mutational analysis-inspired algorithms for cells self-organization towards a dynamic under viability constraints

Author

Abdoulaye Sarr, Alexandra Fronville, Pascal Ballet, Vincent Rodin, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), and Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Computer science, 030303 biophysics, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Morphogenesis, 02 engineering and technology, 03 medical and health sciences, Convergence (routing), 0202 electrical engineering, electronic engineering, information engineering, morphological analysis, [NLIN.NLIN-AO]Nonlinear Sciences [physics]/Adaptation and Self-Organizing Systems [nlin.AO], Organism, biological multi-agent system, Self-organization, 0303 health sciences, business.industry, Cell migration, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Metric space, Order (biology), [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], virtual reality, 020201 artificial intelligence & image processing, Multiplication, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Biological system, business, mathematical programming
Abstract

International audience; In biology, recent techniques in confocal mi- croscopy have produced experimental data which highlights the importance of cellular dynamics in the evolution of biolog- ical shapes. Thus, to understand the mechanisms underlying the morphogenesis of multi-cellular organisms, we study this cellular dynamic system in terms of its properties: cell multi- plication, cell migration, and apoptosis. Besides, understanding the convergence of the system toward a stable form, involves local interactions between cells. Indeed, the way that cells self- organize through these interactions determines the resulting form. Along with the mechanisms of convergence highlighted above, the dynamic system also undergoes controls established by the nature on the organisms growth. Hence, to let the system viable, the global behavior of cells has to be assessed at every state of their developement and must satisfy the constraints. Otherwise, the whole system self-adapts in regard to its global behavior. Thus, we must be able to formalize in a proper metric space a metaphor of cell dynamics in order to find conditions (decisions, states) that would make cells to self-organize and in which cells self-adapt so as to always satisfy operational constraints (such as those induced by the tissue or the use of resources). Therefore, the main point remains to find conditions in which the system is viable and maintains its shape while renewing. The aim of this paper is to explain the mathematical foundations of this work and describe a simulation tool to study the morphogenesis of a virtual organism.

Published
2012

13. An efficient algorithm based on weak synchronization for distributed in virtuo biological experiments

Author

Pascal Ballet, Vincent Rodin, Christophe Le Gal, Gireg Desmeulles, Pascal Redou, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), and Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)

Subjects
Distributed simulation, General Computer Science, Computer science, Multi-agent system, Node (networking), Distributed computing, virtual reality, Complex system, Multi-Agent system, 020206 networking & telecommunications, 02 engineering and technology, peer-to-peer, Virtual reality, Grid, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Metamodeling, Multi-Interaction syste, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Synchronization (computer science), 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC]
Abstract

International audience; Virtual Reality is becoming increasingly necessary to study complex systems such as biological systems. Thanks to Virtual Reality, the user is placed at the heart of biological simulations and can carry out experiments as if he were under the same experimental conditions as in vivo or in vitro. We usually call this kind of experiments in virtuo experiments. In order to rapidly develop Virtual Reality applications related to biology, we have already proposed the RéISCOP meta model which makes it possible to easily design biological simulations and undertake in virtuo experiments. This meta model allows to describe a biological system as a composition of its sub-systems and the interactions between the constituents of these sub-systems. Unfortunately, when using a single computer, the number of simulated entities is far from what is needed in biological simulations. It seemed thus necessary to extend the RéISCOP meta model so that it allows distributed computing on a grid. We made this choice because the structure of the RéISCOP meta model is well adapted to a distribution on a grid where the sub-systems which compose a system can be dispatched on different nodes, the synchronization and the coherence of the system being ensured by a Peer-to-Peer architecture. Unlike traditional approaches which propose a spatial distribution, the method we describe in this paper is based on an "organizational" distribution linked to the RéISCOP meta model. This "organizational" distribution is mainly ensured by using two efficient algorithms based on a dead reckoning method, one for a data consistency between nodes and one for a weak synchronization of the nodes involved. These two algorithms are integrated into the behaviors of agents (DIVAs) which are located on each node of the grid. These agents are able to communicate by using a Peer-to-Peer architecture upon the grid. In order to validate our approach, we implement three distributed simulations with increasing complexities and we compare the results with the results obtained in the non-distributed simulations. We get very similar results for the distributed and the non-distributed simulations.

Published
2011

14. Absolute Stability of Chaotic Asynchronous Multi-Interactions Schemes for Solving ODE

Author

Pascal Redou, Laurent Gaubert, Gireg Desmeulles, Pierre-Antione Béal, Christophe Le Gal, Vincent Rodin, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Lab-STICC_ENIB_CID_IHSEV, Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Université de Brest (UBO), Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), Lab-STICC_UBO_CID_IHSEV, Redou, Pascal, and Gaubert, Laurent

Subjects
Multi-interaction systems, Absolute stability, Random matrices products, Chaotic asynchronous scheduling, Ordi- nary differential systems, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, Ordinary differential systems, [MATH.MATH-NA] Mathematics [math]/Numerical Analysis [math.NA], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA]
Abstract

International audience; Multi Interaction Systems, used in the context of Virtual Reality, are dedicated to real-time interactive simulations. They open the way to the in virtuo experimentation, especially useful in the domain of biochemical kinetics. To this purpose, chaotic and asynchronous scheduling of autonomous processes is based upon desynchronization of phenomena involved in the system. It permits inter- activity, especially the capability to add or remove phenomena in the course of a simulation. It provides methods of resolution of ordinary differential systems and partial derivative equations. Proofs of convergence for these methods have been es- tablished, but the problem of absolute stability, although it is crucial when consid- ering multiscale or stiff problems, has not yet been treated. The aim of this article is to present absolute stability conditions for chaotic and asynchronous schemes. We give criteria so as to predict instability thresholds, and study in details the sig- nificant example of a damped spring-mass system. Our results, which make use of random matrices products theory, stress the point that the desynchronization of phenomena, and a random scheduling of their activations, can lead to instability.

Published
2010

15. MorphoBlock Programming: a way to model and simulate morphogenesis of multicellular organisms

Author

Sébastien Tripodi, Vincent Rodin, Pascal Ballet, Lab-STICC_UBO_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), and Jouglas, Francoise

Subjects
0106 biological sciences, 0303 health sciences, Cell division, business.industry, Multi-agent system, Distributed computing, In silico, MorphoBlock, Morphogenesis, Biology, Bioinformatics, 01 natural sciences, Living systems, 03 medical and health sciences, Multicellular organism, Software, Block (programming), Embryogenesis, business, 030304 developmental biology, 010606 plant biology & botany, Multiagent Systems
Abstract

International audience; Morphogenesis is a key phenomenon occurring in multicellular organisms. It involves many mechanisms at the cellular level like differentiation, migration, division or communication between cells. The study of such complex living systems is difficult despite the improvement of confocal microscopes including those working with four dimensions (space and time). Observation has been much enhanced but comprehension of the organization is yet to come. In virtuo simulation allows focus on the study of the organization mechanisms (in virtuo is an extension of the in silico paradigm where the user is a central actor of the simulation). Hence, the use of a computer program reproducing some parts of the morphogenesis phenomenon is complementary to real experimentation. Moreover, modelling using a programming language facilitates exchange of knowledge between biologists by reducing the ambiguity compared with text or diagrams. To help the comprehension of morphogenesis, we have developed software based on a multiagent system that reproduces the following mechanisms: cell migration, cell division, cell apoptosis, cell signalling, cell differentiation and cell polarization. In our software, an agent is called a MorphoBlock, which means a block of morphogenesis. By using these simple MorphoBlocks, the simulations show different kinds of dynamics and generate structures that can be compared, from an abstract point of view, to the formation of multicellular organisms. In this paper, we focus on two main parts of our software: first the shape, behaviour and parameters of a MorphoBlock; and second the observation of morphogenesis from simulations with many MorphoBlocks.

Published
2009

16. Formal validation of asynchronous interaction-agents algorithms for reaction-diffusion problems

Author

Gireg Desmeulles, Sebastien Kerdelo, Vincent Rodin, Jean-François Abgrall, Pascal Redou, Jacques Tisseau, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Génétique moléculaire et génétique épidémiologique, Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'hématologie biologique, Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Lab-STICC_UBO_CID_IHSEV, Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Lab-STICC_ENIB_CID_IHSEV, and Redou, Pascal

Subjects
0303 health sciences, Mathematical optimization, Context model, Theoretical computer science, Computer science, Multi-agent system, Complex system, Context (language use), 02 engineering and technology, [MATH.MATH-NA] Mathematics [math]/Numerical Analysis [math.NA], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science::Multiagent Systems, 03 medical and health sciences, Asynchronous communication, Reaction–diffusion system, Convergence (routing), 0202 electrical engineering, electronic engineering, information engineering, Partial derivative, 020201 artificial intelligence & image processing, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation, [MATH.MATH-NA]Mathematics [math]/Numerical Analysis [math.NA], 030304 developmental biology
Abstract

International audience; In the context of biological complex systems multi- agent simulation, we present an interaction-agent model for reaction-diffusion problems that enables interaction with the simulation during the execution, and we establish a mathematical validation for our model. We use two types of interaction-agents: on one hand, in a chemical reactor with no spatial dimension -e.g. a cell-, a reaction-agent rep- resents an autonomous chemical reaction between several reactants, and modifies the concentration of reaction prod- ucts. On the other hand, we use interface-agents in order to take into account the spatial dimension that appears with diffusion : interface-agents achieve the matching transfer of reactants between cells. This approach, where the simula- tion engine makes agents intervene in a chaotic and asyn- chronous way, is an alternative to the classical model - which is not relevant when the limits conditions are fre- quently modified- based on partial derivative equations. We enounciate convergence results for our interaction-agent methods, and illustrate our model with an example about coagulation inside a blood vessel.

Published
2007

17. The Virtual Reality applied to the biology understanding: the in virtuo experimentation

Author

Laurent Misery, Pascal Redou, Jacques Tisseau, Gireg Desmeulles, Vincent Rodin, Gabriel Querrec, Sebastien Kerdelo, Laboratoire d'Informatique des Systèmes Complexes (LISYC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), Centre Européen de Réalité Virtuelle (CERV), École Nationale d'Ingénieurs de Brest (ENIB), Service de dermatologie-CHU Morvan, Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Lab-STICC_ENIB_CID_IHSEV, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), and Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Computer science, media_common.quotation_subject, Systems biology, Autonomous agent, Complex system, 02 engineering and technology, Virtual reality, computer.software_genre, 03 medical and health sciences, Artificial Intelligence, Human–computer interaction, 0202 electrical engineering, electronic engineering, information engineering, 030304 developmental biology, media_common, 0303 health sciences, Interactions reification, Multi-agent system, Multi-agent systems, ACM, General Engineering, Reification (computer science), [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Expert system, Fuzzy cognitive map, Computer Science Applications, 020201 artificial intelligence & image processing, In virtuo, computer, Autonomy
Abstract

International audience; The advent of the computer and computer science, and in particular virtual reality, offers new experiment possibilities with numerical simulations and introduces a new type of investigation for the complex systems study: the in virtuo experiment. This work lies on the framework of multi-agent systems. We propose a generic model for systems biology based on reification of the interactions, on a concept of organization and on a multi-model approach. By 'reification' we understand that interactions are considered as autonomous agents. The aim has been to combine the systemic paradigm and the virtual reality to provide an application able to collect, simulate, experiment and understand the knowledge owned by different biologists working around an interdisciplinary subject. Here, we have been focused on the urticaria disease understanding. Autonomy is taken as a principle. The method permits to integrate different natures of model in the same application using chaotic asynchronous iterations and C++ library: AReVi. We have modeled biochemical reactions, molecular 3D diffusion, cell organizations and mechanical 3D interactions. It also permits to embed different expert system modeling methods like fuzzy cognitive maps. This work provides a toolbox easily adaptable to new biological studies.

Published
2006

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