hydroroot

Simulation of hydraulic root architecture

https://github.com/openalea/hydroroot

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • 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
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (10.0%) to scientific vocabulary

Keywords

arabidopsis-thaliana hydraulic-modeling openalea root root-system
Last synced: 4 months ago · JSON representation ·

Repository

Simulation of hydraulic root architecture

Basic Info
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 3
  • Open Issues: 7
  • Releases: 2
Topics
arabidopsis-thaliana hydraulic-modeling openalea root root-system
Created over 4 years ago · Last pushed 4 months ago
Metadata Files
Readme Changelog License Citation Authors Codemeta

README.md

HydroRoot

CI status Documentation Status image

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.

Alt Text

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

https://hydroroot.rtfd.io

Citations

If you use Hydroroot for your research, please cite:

  1. 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
  2. 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

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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      "familyName": "Dr. Boursiac",
      "givenName": "Yann"
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    {
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      "@type": "Person",
      "familyName": "Dr. Lucas",
      "givenName": "Mikael"
    },
    {
      "@id": "https://orcid.org/0000-0002-3293-4049",
      "@type": "Person",
      "familyName": "Dr. Bauget",
      "givenName": "Fabrice"
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    {
      "@id": "https://orcid.org/0000-0002-1202-8460",
      "@type": "Person",
      "familyName": "Dr. Godin",
      "givenName": "Christophe"
    },
    {
      "@id": "https://orcid.org/0000-0002-4255-6440",
      "@type": "Person",
      "familyName": "Dr. Maurel",
      "givenName": "Christophe"
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  ],
  "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

All Time
  • Total Commits: 6,476
  • Total Committers: 51
  • Avg Commits per committer: 126.98
  • Development Distribution Score (DDS): 0.788
Past Year
  • Commits: 12
  • Committers: 2
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.417
Top Committers
Name Email 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...

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
release2025 (4) documentation (2) enhancement (2) bug (1) release refactoring (1) refactoring (1) question (1)
Pull Request Labels

Dependencies

.github/workflows/conda-package-build.yml actions
  • actions/checkout v3 composite
  • haya14busa/action-cond v1 composite
  • openalea/action-build-publish-anaconda v0.1.4 composite