PlanktonIndividuals.jl
PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model - Published in JOSS (2022)
Science Score: 95.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
3 of 4 committers (75.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Repository
This package simulates the behaviors of an ensemble of phytoplankton individuals.
Basic Info
Statistics
- Stars: 33
- Watchers: 7
- Forks: 7
- Open Issues: 4
- Releases: 44
Metadata Files
README.md
PlanktonIndividuals.jl
PlanktonIndividuals.jl is a fast individual-based model written in Julia that can be run on both CPU and GPU. It simulates the life cycle of phytoplankton cells as Lagrangian particles in the ocean while nutrients are represented as Eulerian, density-based tracers using a 3rd order advection scheme. The model is used to simulate and interpret the temporal and spacial variations of phytoplankton cell densities and stoichiometry as well as growth and division behaviors induced by diel cycle and physical motions ranging from sub-mesoscale to large scale processes.
Installation
To add PlanktonIndividuals.jl to your Julia environment:
julia
using Pkg; Pkg.add("PlanktonIndividuals.jl")
Use Examples
1. Simple Flow Fields In Two Dimensions
```julia using PlanktonIndividuals p = dirname(pathof(PlanktonIndividuals))
include(joinpath(p,"../examples/vertical2Dexample.jl"))
include(joinpath(p,"../examples/horizontal2Dexample.jl")) ```
2. Closer Look Into One Grid Box
julia
using PlanktonIndividuals
p = dirname(pathof(PlanktonIndividuals))
include(joinpath(p,"../examples/0D_experiment.jl"))
3. Turbulent Flow Fields In Three Dimensions
Here Oceananigans.jl is used to generate velocity fields and then use those to drive the individual-based model.
julia
using PlanktonIndividuals
p = dirname(pathof(PlanktonIndividuals))
include(joinpath(p,"../examples/surface_mixing_3D_example.jl"))
Owner
- Name: JuliaOcean
- Login: JuliaOcean
- Kind: organization
- Repositories: 10
- Profile: https://github.com/JuliaOcean
JOSS Publication
PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model
Authors
Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology
Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology
Editor
Jayaram Hariharan
Tags
Individual-based model Lagrangian particles phytoplankton biogeochemistry GPU supportGitHub Events
Total
- Create event: 10
- Commit comment event: 4
- Release event: 2
- Watch event: 3
- Delete event: 6
- Issue comment event: 2
- Push event: 46
- Pull request event: 11
- Fork event: 2
Last Year
- Create event: 10
- Commit comment event: 4
- Release event: 2
- Watch event: 3
- Delete event: 6
- Issue comment event: 2
- Push event: 46
- Pull request event: 11
- Fork event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| zhenwu0728 | z****u@m****u | 887 |
| gaelforget | g****t@m****u | 60 |
| Zhen Wu | z****u@W****l | 2 |
| CompatHelper Julia | c****y@j****g | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 12
- Total pull requests: 76
- Average time to close issues: 4 months
- Average time to close pull requests: 5 days
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 7.17
- Average comments per pull request: 0.33
- Merged pull requests: 68
- Bot issues: 0
- Bot pull requests: 9
Past Year
- Issues: 0
- Pull requests: 13
- Average time to close issues: N/A
- Average time to close pull requests: 9 days
- Issue authors: 0
- Pull request authors: 2
- Average comments per issue: 0
- Average comments per pull request: 0.08
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 4
Top Authors
Issue Authors
- zhenwu0728 (6)
- Atreyu-94 (4)
- JuliaTagBot (1)
- gaelforget (1)
Pull Request Authors
- zhenwu0728 (61)
- gaelforget (20)
- github-actions[bot] (13)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- julia 4 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 43
juliahub.com: PlanktonIndividuals
This package simulates the behaviors of an ensemble of phytoplankton individuals.
- Documentation: https://docs.juliahub.com/General/PlanktonIndividuals/stable/
- License: MIT
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Latest release: 0.7.5
published 11 months ago
Rankings
Dependencies
- julia-actions/setup-julia latest composite
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- julia-actions/julia-processcoverage v1 composite
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