rhizodep
Rhizodep is a FSP model designed to simulate rhizodeposition processes
Science Score: 67.0%
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○Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary
Keywords
Repository
Rhizodep is a FSP model designed to simulate rhizodeposition processes
Basic Info
Statistics
- Stars: 4
- Watchers: 5
- Forks: 2
- Open Issues: 2
- Releases: 1
Topics
Metadata Files
README.md
OpenAlea.RhizoDep : a Functional-Structural Root Model to simulate rhizodeposition
Authors: Frederic Rees, Tristan Gerault, Marion Gauthier, Christophe Pradal3
Licence: CeCILL-C
Status: An OpenAlea Python package
About
Model description
RhizoDep is a functional-structural root model aiming to simulate root growth, respiration and rhizodeposition along the whole root system. Root growth is based on a potential growth model adapted from ArchiSimple model, which is regulated by the local balance of carbon in each root segment. This local carbon balance also enables to simulate root respiration, which originates from growth and maintenance, and rhizodeposition, which has been represented as the net exudation of hexose, the secretion of mucilage and the release of cap cells. The model depends on i) the input of carbon allocated from the shoots to the roots, ii) the temperature of the soil, iii) the dynamics of rhizodeposits at the root-soil interface, which is currently simulated by a simple soil degradation function.
Package description
The folder ‘src/openalea/rhizodep’ contains the main files for running RhizoDep, including ‘model.py’ that contains the main code of the model, ‘parameters.py’ that contains default values of parameters, and ‘runningsimulation.py’ that allows to run a complete simulation. Additional scripts in the subfolder ‘tool’ allow plotting the root system computing different variables within the root system. The file ‘runningscenarios.py’ allows in particular to run different scenarios, on the basis of the input file ‘scenarioslist’ that is located in tutorial/inputs. A rapid test of the model can be launched with the file ‘testrhizodep.py’ in the folder ‘test’.
Installation
bash
mamba install -c openalea3 -c conda-forge openalea.rhizodep
Contributors
Owner
- Name: OpenAlea
- Login: openalea
- Kind: organization
- Website: http://openalea.rtfd.io
- Repositories: 54
- Profile: https://github.com/openalea
OpenAlea is an open source project aimed at the plant research community. It includes modules to analyse and model growth and functioning of plant architectures
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: RhizoDep
message: >-
RhizoDep is a model designed to simulate root architecture
and rhizodeposition processes according to root carbon balance.
type: software
authors:
- given-names: Frédéric
family-names: Rees
orcid: 'https://orcid.org/0000-0002-4827-4452'
affiliation: INRAE
- given-names: Tristan
family-names: Gérault
affiliation: INRAE
email: tristan.gerault@inrae.fr
- given-names: Marion
family-names: Gauthier
orcid: 'https://orcid.org/0000-0001-7671-5406'
- given-names: Christophe
family-names: Pradal
affiliation: CIRAD / inria
orcid: 'https://orcid.org/0000-0002-2555-761X'
repository-code: 'https://github.com/openalea/rhizodep'
abstract: >-
RhizoDep is a functional-structural root model that
simulates 3D root growth, respiration, and rhizodeposition
based on carbon balance and root morphology at the individual
root segment level.
keywords:
- openalea
- FSPM
- rhizodeposition
- root system architecture
- carbon
- wheat
license: CECILL-C
GitHub Events
Total
- Create event: 6
- Release event: 1
- Issues event: 5
- Watch event: 3
- Delete event: 2
- Issue comment event: 5
- Push event: 27
- Public event: 1
- Pull request review event: 1
- Pull request event: 7
- Fork event: 1
Last Year
- Create event: 6
- Release event: 1
- Issues event: 5
- Watch event: 3
- Delete event: 2
- Issue comment event: 5
- Push event: 27
- Public event: 1
- Pull request review event: 1
- Pull request event: 7
- Fork event: 1
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 4
- Total pull requests: 4
- Average time to close issues: 8 days
- Average time to close pull requests: 4 days
- Total issue authors: 1
- Total pull request authors: 2
- Average comments per issue: 0.25
- Average comments per pull request: 0.75
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 4
- Pull requests: 4
- Average time to close issues: 8 days
- Average time to close pull requests: 4 days
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 0.25
- Average comments per pull request: 0.75
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- pradal (4)
Pull Request Authors
- pradal (3)
- frees86 (1)
Top Labels
Issue Labels
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Dependencies
- imageio *
- matplotlib *
- numpy *
- pandas *
- path *
- pillow *
- pytest *
- pytest-mock *
- setuptools *