Bvpy
Manuel Petit, Olivier Ali, Florian Gacon, Guillaume Cerutti, Adrien Heymans, Jonathan Legrand, Gonzalo Revilla (Inria project team Mosaic)
Overview
| Model category | ODE |
|---|---|
| Plant part | Any |
| Scale | Organ, Cell |
| Licence | LGPL |
| Operating system | Linux, Maco |
| Programming language | Python |
| Format of model inputs and outputs | Parameters |
| Species studied | Any |
| Execution environment | Python |
| Modelling environment |
Scientific article
BVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology.Florian Gacon,Christophe Godin,Olivier AliJournal of Open Source Software, 2021 View paper
Model description
Initially built up in the context of developmental biology and morphomechanics, Bvpy proposes an intuitive API as close as possible to the formal definition of BVPs. Its purpose is to enable users to quickly and efficiently estimate the behavior of a wide variety of fields (scalars, vectors, tensors) on biologically relevant structures (Riemannian and non-Rieamannian manifolds), inspired by biophysical and biochemical processes (morphogene patterning, active matter mechanics, diffusion-reaction processes, active transports…).
Some case studies
Conserved mechanical hallmark guides four-way junction avoidance during plant cytokinesis
https://www.cell.com/current-biology/fulltext/S0960-9822(25)00510-X
Similar models
Other models for the simulation of Any: