Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
18 of 51 committers (35.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Keywords
Repository
Simulation of hydraulic root architecture
Basic Info
- Host: GitHub
- Owner: openalea
- License: other
- Language: Python
- Default Branch: main
- Homepage: https://hydroroot.readthedocs.io
- Size: 61.9 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 3
- Open Issues: 7
- Releases: 2
Topics
Metadata Files
README.md
HydroRoot
Software
Authors
- Christophe Pradal
- Yann Boursiac
- Mikael Lucas
- Fabrice Bauget
- Christophe Godin
- Christophe Maurel
Institutes
CIRAD / INRAE / inria / CNRS
Status
Python package
License
CecILL-C
URL : https://hydroroot.rtfd.io
About
Description
OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package.
Content
The OpenAlea.HydroRoot package contains a root architecture simulation model coupled with a water and solute transport solver. It contains a pure hydraulic solver that is solved using resistance network analogy. It also contains a water and solute transport solver that is more complex and see the root as a continuous medium.
Example
Heat map representation of the incoming local radial flows on an arabidopsis root.

Installation
Conda Installation
conda create -n hydroroot -c conda-forge -c openalea3 openalea.hydroroot
Requirements
- openalea.mtg
- openalea.plantgl
- RSML
- pandas > 0.17
- numpy
- scipy
Usage
See notebook in example directory.
Documentation
Citations
If you use Hydroroot for your research, please cite:
- Yann Boursiac, Christophe Pradal, Fabrice Bauget, Mikaël Lucas, Stathis Delivorias, Christophe Godin, Christophe Maurel, Phenotyping and modeling of root hydraulic architecture reveal critical determinants of axial water transport, Plant Physiology, Volume 190, Issue 2, October 2022, Pages 1289--1306, https://doi.org/10.1093/plphys/kiac281
- Fabrice Bauget, Virginia Protto, Christophe Pradal, Yann Boursiac, Christophe Maurel, A root functional--structural model allows assessment of the effects of water deficit on water and solute transport parameters, Journal of Experimental Botany, Volume 74, Issue 5, 13 March 2023, Pages 1594--1608, https://doi.org/10.1093/jxb/erac471
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: OpenAlea.HydroRoot
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- name-particle: Dr.
family-names: Pradal
given-names: Christophe
orcid: 'https://orcid.org/0000-0002-2555-761X'
- family-names: Boursiac
given-names: Yann
orcid: 'https://orcid.org/0000-0002-9545-9003'
name-particle: Dr.
- family-names: Lucas
given-names: Mikael
orcid: 'https://orcid.org/0000-0001-6286-7759'
name-particle: Dr.
- family-names: Bauget
given-names: Fabrice
name-particle: Dr.
orcid: 'https://orcid.org/0000-0002-3293-4049'
- name-particle: Dr.
family-names: Godin
orcid: 'https://orcid.org/0000-0002-1202-8460'
given-names: Christophe
- name-particle: Dr.
family-names: Maurel
given-names: Christophe
orcid: 'https://orcid.org/0000-0002-4255-6440'
abstract: >-
OpenAlea.HydroRoot is a hydraulic root architecture
modelling and a root architecture system generator
package.
keywords:
- root
- openalea
- hydraulic
- maize
- arabidopsis
- millet
license: CECILL-C
preferred-citation:
type: article
authors:
- family-names: Boursiac
given-names: Yann
orcid: 'https://orcid.org/0000-0002-9545-9003'
- family-names: Pradal
given-names: Christophe
email: christophe.pradal@cirad.fr
orcid: 'https://orcid.org/0000-0002-2555-761X'
- family-names: Bauget
given-names: Fabrice
orcid: 'https://orcid.org/0000-0002-3293-4049'
- family-names: Lucas
given-names: Mikael
orcid: 'https://orcid.org/0000-0001-6286-7759'
- family-names: Delivorias
given-names: Stathis
orcid: 'https://orcid.org/0000-0003-4443-4022'
- family-names: Godin
orcid: 'https://orcid.org/0000-0002-1202-8460'
given-names: Christophe
- family-names: Maurel
given-names: Christophe
orcid: 'https://orcid.org/0000-0002-4255-6440'
title: "Phenotyping and modeling of root hydraulic architecture reveal critical determinants of axial water transport"
doi: "10.1093/plphys/kiac281"
journal: "Plant Physiology"
year: 2022
volume: 190
issue: 2
start: 1289 # First page number
end: 1306 # Last page number
CodeMeta (codemeta.json)
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"@type": "SoftwareSourceCode",
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"familyName": "Dr. Boursiac",
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},
{
"@id": "https://orcid.org/0000-0001-6286-7759",
"@type": "Person",
"familyName": "Dr. Lucas",
"givenName": "Mikael"
},
{
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"@type": "Person",
"familyName": "Dr. Bauget",
"givenName": "Fabrice"
},
{
"@id": "https://orcid.org/0000-0002-1202-8460",
"@type": "Person",
"familyName": "Dr. Godin",
"givenName": "Christophe"
},
{
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"@type": "Person",
"familyName": "Dr. Maurel",
"givenName": "Christophe"
}
],
"description": "OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package.",
"keywords": [
"root",
"openalea",
"hydraulic",
"maize",
"arabidopsis",
"millet"
],
"license": "https://spdx.org/licenses/CECILL-C",
"name": "OpenAlea.HydroRoot"
}
GitHub Events
Total
- Issues event: 20
- Delete event: 11
- Issue comment event: 17
- Push event: 71
- Pull request review comment event: 9
- Pull request review event: 13
- Pull request event: 55
- Create event: 10
Last Year
- Issues event: 20
- Delete event: 11
- Issue comment event: 17
- Push event: 71
- Pull request review comment event: 9
- Pull request review event: 13
- Pull request event: 55
- Create event: 10
Committers
Last synced: almost 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Pierre Fernique | p****e@i****r | 1,374 |
| Frederic Boudon | f****n@c****r | 861 |
| Christophe Pradal | c****l@i****r | 749 |
| Julien Diener | j****r@g****m | 468 |
| Chakkrit Preuksakarn | p****t@g****m | 392 |
| Jean-Baptiste Durand | J****d@i****r | 360 |
| Jean Peyhardi | j****i@g****m | 252 |
| Mathilde Balduzzi | m****i@i****r | 243 |
| Yann Guédon | g****n@c****r | 238 |
| Samuel Dufour-Kowalski | s****r@c****r | 156 |
| Romain Fernandez | r****6@g****m | 151 |
| Alexandra Jestin | a****n@i****r | 149 |
| Eric Moscardi | e****i@g****m | 134 |
| Thomas Cokelaer | c****r@g****m | 117 |
| Pascal Ferraro | p****o@l****r | 101 |
| Christophe Godin | c****n@i****r | 83 |
| Daniel Barbeau | d****u@s****r | 83 |
| baugetfa | f****t@s****r | 43 |
| Julien Coste | j****e@i****r | 38 |
| Pierre Barbier de Reuille | p****e@g****m | 36 |
| Anne-Sarah Briand | a****d@h****r | 36 |
| Severine | n****r@c****r | 35 |
| Unknown Author | n****r@i****r | 31 |
| Mikaël Lucas | m****s@e****g | 30 |
| Matthias Puech | p****h@c****t | 30 |
| Guillaume Cerutti | g****i@i****r | 29 |
| Aida Ouangraoua | o****o@l****r | 29 |
| Mahmoud Omidvar | o****d@g****m | 27 |
| Adama Ndour | a****p@g****m | 25 |
| Gabriel Radanne | y****g@n****r | 24 |
| and 21 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 19
- Total pull requests: 42
- Average time to close issues: 8 months
- Average time to close pull requests: 1 day
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 0.58
- Average comments per pull request: 0.21
- Merged pull requests: 32
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 13
- Pull requests: 31
- Average time to close issues: 3 days
- Average time to close pull requests: about 13 hours
- Issue authors: 3
- Pull request authors: 2
- Average comments per issue: 0.54
- Average comments per pull request: 0.06
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- baugetfa (9)
- pradal (8)
- AurelienBesnier (2)
Pull Request Authors
- baugetfa (30)
- pradal (9)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v3 composite
- haya14busa/action-cond v1 composite
- openalea/action-build-publish-anaconda v0.1.4 composite