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Valérie Lobjois
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Proceedings Papers
ISiCell: A Participatory Methodology and Platform for Collaborative Agent-Based Modeling in Cell Biology
Open Access
. isal2024, ALIFE 2024: Proceedings of the 2024 Artificial Life Conference46, (July 22–26, 2024) 10.1162/isal_a_00769
Abstract
View Papertitled, ISiCell: A Participatory Methodology and Platform for Collaborative Agent-Based Modeling in Cell Biology
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for content titled, ISiCell: A Participatory Methodology and Platform for Collaborative Agent-Based Modeling in Cell Biology
Agent-based models are widely used in biology to study tissue-scale phenomena by simulating individual cell behaviors, offering insights into cellular biology and serving as predictive tools through computer simulations. However, their development requires effective communication between biologists and modelers, leading to delays. To address this, we propose a novel methodology using Unified Modeling Language (UML) diagrams to enhance communication and involve biologists in the model design process. These diagrams provide clarity and structure, while simulation visualization gathers qualitative feedback for validation. We also introduce a web platform allowing the creation of UML diagrams and automatic code translation for immediate simulation visualization. This article demonstrates our platform’s capability by replicating two models from literature.
Proceedings Papers
Checkpoint Orientated Cell Cycle Modeling Issues in Simulation of Synchronized Situation
Open Access
. alife2012, ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems465-472, (July 19–22, 2012) 10.1162/978-0-262-31050-5-ch061
Proceedings Papers
A checkpoint-orientated model to simulate unconstrained proliferation of cells (full article)
Open Access
. ecal2011, ECAL 2011: The 11th European Conference on Artificial Life96, (August 8–12, 2011) 10.7551/978-0-262-29714-1-ch096