AIBECS.jl

AIBECS.jl: A tool for exploring global marine biogeochemical cycles. - Published in JOSS (2022)

Science Score: 100.0%

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 12 DOI reference(s) in README and JOSS metadata
○
Academic publication links
✓
Committers with academic emails
1 of 3 committers (33.3%) from academic institutions
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

awesome biogeochemical biogeochemical-model biogeochemistry fluxes global inverse-model julia marine marine-tracer model modeling models ocean ocean-circulation oceanography optimization pathways tracer transport

Keywords from Contributors

surrogate pde standardization

Last synced: 4 months ago · JSON representation ·

Repository

The ideal tool for exploring global marine biogeochemical cycles.

Basic Info

Host: GitHub
Owner: JuliaOcean
License: mit
Language: Julia
Default Branch: master
Size: 371 MB

Statistics

Stars: 40
Watchers: 3
Forks: 7
Open Issues: 32
Releases: 102

Topics

Created over 6 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation Zenodo

ReadMe.md

AIBECS.jl

The ideal tool for exploring global marine biogeochemical cycles.

AIBECS (for Algebraic Implicit Biogeochemical Elemental Cycling System, pronounced like the cool ibex) is a Julia package that provides ocean biogeochemistry modellers with an easy-to-use interface for creating and running models of the ocean system.

AIBECS is a system because it allows you to choose some biogeochemical tracers, define their interactions, select an ocean circulation and Voilà! — your model is ready to run.

Getting started

If you are new to AIBECS, head over to the documentation and look for the tutorials. (You can also click on the big "Documentation" badge above.)

Concept

This package was developed to exploit linear-algebra tools and algorithms in Julia to efficiently simulate marine tracers. AIBECS represents global biogeochemical cycles with a discretized system of nonlinear ordinary differential equations that takes the generic form

$$\frac{∂\boldsymbol{x}}{∂t} + \mathbf{T} \boldsymbol{x} = \boldsymbol{G}(\boldsymbol{x})$$

where $\boldsymbol{x}$ represents the model state variables, i.e., the marine tracer(s) concentration. For a single tracer, $\boldsymbol{x}$ can be interpreted as the 3D field of its concentration. In AIBECS, $\boldsymbol{x}$ is represented as a column vector (that's why it's bold and italic).

The operator $\mathbf{T}$ is a spatial differential operator that represents the transport of tracers. For example, for a single tracer transported by ocean circulation,

$$\mathbf{T} = \nabla \cdot(\boldsymbol{u} - \mathbf{K}\nabla)$$

represents the effects of advection and eddy-diffusion (where $\boldsymbol{u}$ is the 3D vector of the marine currents and $\mathbf{K}$ is a 3×3 eddy-diffusivity matrix). Thus, $\mathbf{T}$ "acts" on $\boldsymbol{x}$ such that $\mathbf{T}\boldsymbol{x}$ is the flux divergence of that tracer. In AIBECS, $\mathbf{T}$ is represented by a matrix (that's why it's bold and upstraight).

Lastly, the right-hand-side, $\boldsymbol{G}(\boldsymbol{x}$), represents the local sources minus sinks of each tracer, which must be provided as functions of the tracer(s) $\boldsymbol{x}$.

To simulate tracers using the AIBECS, you just need to define the transport operators $\mathbf{T}$ and the net sources and sinks $\boldsymbol{G}$. That's pretty much the whole concept!

Note on maintenance and development

Note that AIBECS is essentially in maintenance-only mode, and might remain so for a little while. Although it works (the software has been published and has been used in publications), I consider AIBECS still in development, with a bunch of features and fixes that are currently missing, but I do not have enough time to work on it unfortunately. Please get in touch if you have some bandwidth and/or funding and are interested in collaborating or developing AIBECS!

References

This code is © Benoît Pasquier (2024) and contributors, and it is made available under the MIT license enclosed with the software.

Over and above the legal restrictions imposed by this license, if you use this software for an academic publication then you are obliged to provide proper attribution. This can be to this code directly,

Benoît Pasquier, François W. Primeau, and Seth G. John (2024). AIBECS.jl: A tool for exploring global marine biogeochemical cycles. Zenodo. doi: 10.5281/zenodo.2864051.

or to the paper that describes it,

Benoît Pasquier, François W. Primeau, and Seth G. John (2022). AIBECS.jl: A tool for exploring global marine biogeochemical cycles. doi: 10.21105/joss.03814

or (ideally) both. You can also find the citation(s) in BibTeX format in the CITATION.bib file.

If you use data provided by this package (like the ocean circulation from the OCIM), please cite them as well.

Also, if you want to do research using the AIBECS, and you think I could help, do not hesitate to contact me directly (contacts on my website), I would be happy to contribute and collaborate!

NSF

The authors acknowledge funding from the Department of Energy grant DE-SC0016539 and from the National Science Foundation grant 1658380.

Owner

Name: JuliaOcean
Login: JuliaOcean
Kind: organization

Repositories: 10
Profile: https://github.com/JuliaOcean

JOSS Publication

AIBECS.jl: A tool for exploring global marine biogeochemical cycles.

Published

January 05, 2022

DOI

10.21105/joss.03814

Volume 7, Issue 69, Page 3814

Authors

Benoît Pasquier

Department of Earth Sciences, University of Southern California, (now at) School of Mathematics and Statistics, University of New South Wales, Sydney

François W. Primeau

Department of Earth System Science, University of California, Irvine

Seth G. John

Department of Earth Sciences, University of Southern California

Editor

Kristen Thyng

Citation (CITATION.bib)

             _____   ____    ______    _____    _____
     /\     |_   _| |  _ \  |  ____|  / ____|  / ____|
    /  \      | |   | |_) | | |__    | |      | (___
   / /\ \     | |   |  _ <  |  __|   | |       \___ \
  / ____ \   _| |_  | |_) | | |____  | |____   ____) |
 /_/    \_\ |_____| |____/  |______|  \_____| |_____/

Main citations: AIBECS software
@misc{AIBECS.jl,
    author = {Pasquier, Benoît and Primeau, François W. and John, Seth G.},
    title = {{{AIBECS}}.Jl: {{A}} Tool for Exploring Global Marine Biogeochemical Cycles.},
    year = 2024,
    doi = {10.5281/zenodo.2864051.},
}
AIBECS JOSS paper
@article{Pasquier_etal_JOSS_2022,
    title = {{{AIBECS}}.Jl: {{A}} Tool for Exploring Global Marine Biogeochemical Cycles.},
    author = {Pasquier, Benoît and Primeau, François W. and John, Seth G.},
    year = {2022},
    journal = {Journal of Open Source Software},
    volume = {7},
    number = {69},
    pages = {3814},
    publisher = {The Open Journal},
    doi = {10.21105/joss.03814}
}

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   _____   _____   _____     _____   _    _   _                   _______   _____    ____    _   _    _____
  / ____| |_   _| |  __ \   / ____| | |  | | | |          /\     |__   __| |_   _|  / __ \  | \ | |  / ____|
 | |        | |   | |__) | | |      | |  | | | |         /  \       | |      | |   | |  | | |  \| | | (___
 | |        | |   |  _  /  | |      | |  | | | |        / /\ \      | |      | |   | |  | | | . ` |  \___ \
 | |____   _| |_  | | \ \  | |____  | |__| | | |____   / ____ \     | |     _| |_  | |__| | | |\  |  ____) |
  \_____| |_____| |_|  \_\  \_____|  \____/  |______| /_/    \_\    |_|    |_____|  \____/  |_| \_| |_____/

OCIM0
@article{Primeau_etal_2013,
    AUTHOR = "F. W. Primeau and M. Holzer and T. DeVries",
    TITLE = {{S}outhern {O}cean nutrient trapping and the efficiency of the biological pump},
    JOURNAL = {Journal of Geophysical Research},
    VOLUME = "118",
    doi = "10.1002/jgrc.20181",
    PAGES = "2547-2564",
    YEAR = "2013"
}

OCIM1
@article{DeVries_2014,
    author = {DeVries, Tim},
    title = {The oceanic anthropogenic {CO}\textsubscript{2} sink: Storage, air-sea fluxes, and transports over the industrial era},
    journal = {Global Biogeochemical Cycles},
    volume = {28},
    number = {7},
    issn = {1944-9224},
    doi = {10.1002/2013GB004739},
    pages = {631--647},
    year = {2014},
}
@article{DeVries_Primeau_2011,
    TITLE="Dynamically and Observationally Constrained Estimates of Water-Mass Distributions and Ages in the Global Ocean",
    AUTHOR = "DeVries, Tim and Primeau, Fran\c{c}ois",
    JOURNAL = "Journal of Physical Oceanography",
    YEAR = "2011",
    pages = "2381--2401",
    VOLUME = "41",
    doi = "10.1175/JPO-D-10-05011.1",
}

Archer_etal_2000 3-box model
@article{Archer_etal_2000,
    author = {Archer, David E. and Eshel, Gidon and Winguth, Arne and Broecker, Wallace and Pierrehumbert, Ray and Tobis, Michael and Jacob, Robert},
    title = {Atmospheric pCO\textsupscript{2} sensitivity to the biological pump in the ocean},
    journal = {Global Biogeochemical Cycles},
    volume = {14},
    number = {4},
    pages = {1219--1230},
    doi = {10.1029/1999GB001216},
    year = {2000}
}

TwoBoxModel
@book{Sarmiento_Gruber_2006,
    author = "J. L. Sarmiento and N. Gruber",
    title = "Ocean Biogeochemical Dynamics",
    pages = "503",
    publisher = "Princeton Univ. Press, Princeton and Oxford",
    year = "2006",
}

OCIM2
@article{DeVries_Holzer_2019,
    author = {DeVries, Tim and Holzer, Mark},
    title = {Radiocarbon and Helium Isotope Constraints on Deep Ocean Ventilation and Mantle-\textsuperscript{3}{He} Sources},
    journal = {Journal of Geophysical Research: Oceans},
    volume = {124},
    number = {5},
    pages = {3036--3057},
    doi = {10.1029/2018JC014716},
    year = {2019}
}

OCIM2_48L
@article{Holzer_etal_2021,
    author = {Holzer, Mark and DeVries, Tim and {de Lavergne}, Casimir},
    year = {2021},
    journal = {Nature Communications},
    volume = {12},
    number = {1},
    pages = {4348},
    issn = {2041-1723},
    doi = {10.1038/s41467-021-24648-x}
}

POP
Coming soon!

MITgcm / OCCA
@article{Forget_2010,
    author = {Forget, Ga\"{e}l},
    title = {Mapping Ocean Observations in a Dynamical Framework: A 2004--06 Ocean Atlas},
    journal = {Journal of Physical Oceanography},
    volume = {40},
    number = {6},
    pages = {1201--1221},
    year = {2010},
    doi = {10.1175/2009JPO4043.1}
}

----------------------------------------------------------------------------------



             ______   _____     ____     _____    ____    _         _____
     /\     |  ____| |  __ \   / __ \   / ____|  / __ \  | |       / ____|
    /  \    | |__    | |__) | | |  | | | (___   | |  | | | |      | (___
   / /\ \   |  __|   |  _  /  | |  | |  \___ \  | |  | | | |       \___ \
  / ____ \  | |____  | | \ \  | |__| |  ____) | | |__| | | |____   ____) |
 /_/    \_\ |______| |_|  \_\  \____/  |_____/   \____/  |______| |_____/

# Chien et al
@article{Chien_etal_2016,
    author = {Chien, Chia-Te and Mackey, Katherine R. M. and Dutkiewicz, Stephanie and Mahowald, Natalie M. and Prospero, Joseph M. and Paytan, Adina},
    title = {Effects of {A}frican dust deposition on phytoplankton in the western tropical {A}tlantic {O}cean off {B}arbados},
    journal = {Global Biogeochemical Cycles},
    volume = {30},
    number = {5},
    pages = {716--734},
    keywords = {atmospheric deposition, Barbados, phytoplankton community structure, nutrient limitation},
    doi = {10.1002/2015GB005334},
    year = {2016}
}

# Kok et al
@article{Kok_etal_2021b,
    author = {Kok, J. F. and Adebiyi, A. A. and Albani, S. and Balkanski, Y. and Checa-Garcia, R. and Chin, M. and Colarco, P. R. and Hamilton, D. S. and Huang, Y. and Ito, A. and Klose, M. and Li, L. and Mahowald, N. M. and Miller, R. L. and Obiso, V. and P\'erez Garc\'{\i}a-Pando, C. and Rocha-Lima, A. and Wan, J. S.},
    title = {Contribution of the world's main dust source regions to the global cycle of desert dust},
    journal = {Atmospheric Chemistry and Physics},
    volume = {21},
    year = {2021},
    number = {10},
    pages = {8169--8193},
    doi = {10.5194/acp-21-8169-2021}
}
@article{Adebiyi_etal_2020,
    author = {Adebiyi, A. A. and Kok, J. F. and Wang, Y. and Ito, A. and Ridley, D. A. and Nabat, P. and Zhao, C.},
    title = {Dust Constraints from joint Observational-Modelling-experiMental analysis
    (dustcoMM): comparison with measurements and model simulations},
    journal = {Atmospheric Chemistry and Physics},
    volume = {20},
    year = {2020},
    number = {2},
    pages = {829--863},
    doi = {10.5194/acp-20-829-2020}
}
@article{Kok_etal_2021a,
    author = {Kok, J. F. and Adebiyi, A. A. and Albani, S. and Balkanski, Y. and Checa-Garcia, R. and Chin, M. and Colarco, P. R. and Hamilton, D. S. and Huang, Y. and Ito, A. and Klose, M. and Leung, D. M. and Li, L. and Mahowald, N. M. and Miller, R. L. and Obiso, V. and P\'erez Garc\'{\i}a-Pando, C. and Rocha-Lima, A. and Wan, J. S. and Whicker, C. A.},
    title = {Improved representation of the global dust cycle using observational constraints on dust properties and abundance},
    journal = {Atmospheric Chemistry and Physics},
    volume = {21},
    year = {2021},
    number = {10},
    pages = {8127--8167},
    doi = {10.5194/acp-21-8127-2021}
}
@article{Scanza_etal_2018,
    author = {Scanza, R. A. and Hamilton, D. S. and Perez Garcia-Pando, C. and Buck, C. and Baker, A. and Mahowald, N. M.},
    title = {Atmospheric processing of iron in mineral and combustion aerosols:
    development of an intermediate-complexity mechanism suitable for Earth
    system models},
    journal = {Atmospheric Chemistry and Physics},
    volume = {18},
    year = {2018},
    number = {19},
    pages = {14175--14196},
    doi = {10.5194/acp-18-14175-2018}
}

----------------------------------------------------------------------------------



  _______    ____    _____     ____     _____   _____               _____    _    _  __     __
 |__   __|  / __ \  |  __ \   / __ \   / ____| |  __ \      /\     |  __ \  | |  | | \ \   / /
    | |    | |  | | | |__) | | |  | | | |  __  | |__) |    /  \    | |__) | | |__| |  \ \_/ /
    | |    | |  | | |  ___/  | |  | | | | |_ | |  _  /    / /\ \   |  ___/  |  __  |   \   /
    | |    | |__| | | |      | |__| | | |__| | | | \ \   / ____ \  | |      | |  | |    | |
    |_|     \____/  |_|       \____/   \_____| |_|  \_\ /_/    \_\ |_|      |_|  |_|    |_|

@article{Amante_Eakins_2009,
    title = {{ETOPO1} 1 arc-minute global relief model: procedures, data sources and analysis},
    author = {Amante, Christopher and Eakins, Barry W},
    year = {2009},
    journal = {NOAA Technical Memorandum NESDIS NGDC-24},
    publisher ={National Geophysical Data Center, NOAA},
    doi = {10.7289/V5C8276M}
}

----------------------------------------------------------------------------------



  _____  _______      ________ _____   _____
 |  __ \|_   _\ \    / /  ____|  __ \ / ____|
 | |__) | | |  \ \  / /| |__  | |__) | (___
 |  _  /  | |   \ \/ / |  __| |  _  / \___ \
 | | \ \ _| |_   \  /  | |____| | \ \ ____) |
 |_|  \_\_____|   \/   |______|_|  \_\_____/

Dataset
@misc{Dai_2017,
    author = "Aiguo {Dai}",
    title = "Dai and Trenberth Global River Flow and Continental Discharge Dataset",
    publisher  = "Research Data Archive at the National Center for Atmospheric Research, Computational and Information Systems Laboratory",
    address = {Boulder CO},
    year  = "2017",
    doi = "10.5065/D6V69H1T"
}

Formal publication that describe the dataset
@article{Dai_Trenberth_2002,
    author = {Dai, Aiguo and Trenberth, Kevin E.},
    title = "{Estimates of Freshwater Discharge from Continents: Latitudinal and Seasonal Variations}",
    journal = {Journal of Hydrometeorology},
    volume = {3},
    number = {6},
    pages = {660--687},
    year = {2002},
    month = {12},
    issn = {1525--755X},
    doi = {10.1175/1525-7541(2002)003<0660:EOFDFC>2.0.CO;2}
}

Descriptions of updates to the dataset
@article{Dai_etal_2009,
    author = {Dai, Aiguo and Qian, Taotao and Trenberth, Kevin E. and Milliman, John D.},
    title = "{Changes in Continental Freshwater Discharge from 1948 to 2004}",
    journal = {Journal of Climate},
    volume = {22},
    number = {10},
    pages = {2773--2792},
    year = {2009},
    month = {05},
    issn = {0894--8755},
    doi = {10.1175/2008JCLI2592.1},
}
@inbook{Dai_2016,
    author = {Dai, Aiguo},
    publisher = {American Geophysical Union (AGU)},
    isbn = {9781118971772},
    title = {Historical and Future Changes in Streamflow and Continental Runoff},
    booktitle = {Terrestrial Water Cycle and Climate Change},
    chapter = {2},
    pages = {17--37},
    doi = {10.1002/9781118971772.ch2},
    year = {2016},
}

----------------------------------------------------------------------------------



   _____ _____   ____  _    _ _   _ _______          __  _______ ______ _____
  / ____|  __ \ / __ \| |  | | \ | |  __ \ \        / /\|__   __|  ____|  __ \
 | |  __| |__) | |  | | |  | |  \| | |  | \ \  /\  / /  \  | |  | |__  | |__) |
 | | |_ |  _  /| |  | | |  | | . ` | |  | |\ \/  \/ / /\ \ | |  |  __| |  _  /
 | |__| | | \ \| |__| | |__| | |\  | |__| | \  /\  / ____ \| |  | |____| | \ \
  \_____|_|  \_\\____/ \____/|_| \_|_____/   \/  \/_/    \_\_|  |______|_|  \_\

Paper
@article{Luijendijk_etal_2020,
    doi = {10.1038/s41467-020-15064-8},
    year = {2020},
    publisher = {Springer Science and Business Media {LLC}},
    volume = {11},
    number = {1},
    author = {Elco Luijendijk and Tom Gleeson and Nils Moosdorf},
    title = {Fresh groundwater discharge insignificant for the world's oceans but important for coastal ecosystems},
    journal = {Nature Communications}
}

Dataset
@misc{luijendijk_etal_2019,
    author={Elco {Luijendijk} and Tom {Gleeson} and Nils {Moosdorf}},
    title={{Geospatial data and model results for a global model study of coastal groundwater discharge}},
    year={2019},
    doi={10.1594/PANGAEA.907641},
    note={Supplement to: Luijendijk, E et al. (2019): The Flow of Fresh Groundwater and Solutes to the World{\textquotesingle}s Oceans and Coastal Ecosystems. EarthArXiv Preprints, https://doi.org/10.31223/osf.io/sw8r4}
    type={data set},
    publisher={PANGAEA}
}

GitHub Events

Total

Create event: 3
Commit comment event: 4
Issues event: 3
Release event: 2
Watch event: 3
Delete event: 1
Issue comment event: 4
Push event: 13
Pull request review event: 1
Pull request event: 2

Last Year

Create event: 3
Commit comment event: 4
Issues event: 3
Release event: 2
Watch event: 3
Delete event: 1
Issue comment event: 4
Push event: 13
Pull request review event: 1
Pull request event: 2

Committers

Last synced: 5 months ago

All Time

Total Commits: 364
Total Committers: 3
Avg Commits per committer: 121.333
Development Distribution Score (DDS): 0.049

Past Year

Commits: 5
Committers: 2
Avg Commits per committer: 2.5
Development Distribution Score (DDS): 0.2

Top Committers

Name	Email	Commits
Benoit Pasquier	p**b@u**u	346
github-actions[bot]	4****]	17
Julia TagBot	5****t	1

Committer Domains (Top 20 + Academic)

uci.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 64
Total pull requests: 37
Average time to close issues: 2 months
Average time to close pull requests: about 12 hours
Total issue authors: 8
Total pull request authors: 3
Average comments per issue: 1.36
Average comments per pull request: 0.92
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 19

Past Year

Issues: 2
Pull requests: 1
Average time to close issues: 2 days
Average time to close pull requests: about 3 hours
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.5
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 1

View more stats

Top Authors

Issue Authors

briochemc (53)
profseth (5)
ChrisRackauckas (1)
zliangocean (1)
stanleesocca (1)
zhenwu0728 (1)
JianghuiDu (1)
JuliaTagBot (1)

Pull Request Authors

github-actions[bot] (20)
briochemc (18)
JuliaTagBot (1)

Top Labels

Issue Labels

enhancement (11) bug (2) help wanted (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- julia 2 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 99

juliahub.com: AIBECS

The ideal tool for exploring global marine biogeochemical cycles.

Documentation: https://docs.juliahub.com/General/AIBECS/stable/
License: MIT
Status: removed
Latest release: 0.13.3
published over 1 year ago

Versions: 99
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 2 Total

Rankings

Dependent repos count: 9.9%

Stargazers count: 16.6%

Forks count: 21.7%

Average: 21.8%

Dependent packages count: 38.9%

Last synced: about 1 year ago

Dependencies

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AIBECS.jl

Science Score: 100.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

ReadMe.md

AIBECS.jl

Getting started

Concept

Note on maintenance and development

References

Owner

JOSS Publication

AIBECS.jl: A tool for exploring global marine biogeochemical cycles.

Authors

Editor

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