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Carbon and Temperature","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\u003ca href=\"https://github.com/JuliaOcean/AIBECS.jl\"\u003e\n  \u003cimg src=\"https://user-images.githubusercontent.com/4486578/60554111-8fc27400-9d79-11e9-9ca7-6d78ee89ea70.png\" alt=\"logo\" title=\"The AIBECS logo: It represents three global marine biogeochemical cycles, where each element affects the others\" align=\"center\" width=\"50%\"/\u003e\n\u003c/a\u003e\n\n# AIBECS.jl\n\n*The ideal tool for exploring global marine biogeochemical cycles.*\n\n\u003cp\u003e\n  \u003ca href=\"https://JuliaOcean.github.io/AIBECS.jl/stable/\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JuliaOcean/AIBECS.jl/docs.yml?style=for-the-badge\u0026label=Documentation\u0026logo=Read%20the%20Docs\u0026logoColor=white\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://doi.org/10.21105/joss.03814\"\u003e\n    \u003cimg src=\"https://img.shields.io/static/v1?label=JOSS\u0026message=10.21105/joss.03814\u0026color=9cf\u0026style=flat-square\" alt=\"DOI badge\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://www.bpasquier.com/talk/osm_sandiego_2020/OSM_SanDiego_2020.pdf\"\u003e\n    \u003cimg src=https://img.shields.io/static/v1?label=Poster\u0026message=OSM2020\u0026color=9cf\u0026style=flat-square\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp\u003e\n  \u003ca href=\"https://doi.org/10.5281/zenodo.2864051\"\u003e\n    \u003cimg src=\"http://img.shields.io/badge/DOI-10.5281%20%2F%20zenodo.2864051-blue.svg?\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://github.com/JuliaOcean/AIBECS.jl/blob/master/LICENSE\"\u003e\n    \u003cimg alt=\"License: MIT\" src=\"https://img.shields.io/badge/License-MIT-blue.svg?\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp\u003e\n  \u003ca href=\"https://github.com/JuliaOcean/AIBECS.jl/actions\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JuliaOcean/AIBECS.jl/mac.yml?label=OSX\u0026logo=Apple\u0026logoColor=white\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://github.com/JuliaOcean/AIBECS.jl/actions\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JuliaOcean/AIBECS.jl/linux.yml?label=Linux\u0026logo=Linux\u0026logoColor=white\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://github.com/JuliaOcean/AIBECS.jl/actions\"\u003e\n    \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JuliaOcean/AIBECS.jl/windows.yml?label=Windows\u0026logo=Windows\u0026logoColor=white\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n  \u003ca href=\"https://codecov.io/gh/JuliaOcean/AIBECS.jl\"\u003e\n    \u003cimg src=\"https://img.shields.io/codecov/c/github/JuliaOcean/AIBECS.jl/master?label=Codecov\u0026logo=codecov\u0026logoColor=white\u0026style=flat-square\"\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\n\n\n**AIBECS** (for **A**lgebraic **I**mplicit **B**iogeochemical **E**lemental **C**ycling **S**ystem, pronounced like the cool [ibex](https://en.wikipedia.org/wiki/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.\n\nAIBECS 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.\n\n## Getting started\n\nIf you are new to AIBECS, head over to the [documentation](https://JuliaOcean.github.io/AIBECS.jl/stable/) and look for the tutorials.\n(You can also click on the big \"Documentation\" badge above.)\n\n## Concept\n\nThis package was developed to exploit linear-algebra tools and algorithms in Julia to efficiently simulate marine tracers.\nAIBECS represents global biogeochemical cycles with a discretized system of nonlinear ordinary differential equations that takes the generic form\n\n$$\\frac{∂\\boldsymbol{x}}{∂t} + \\mathbf{T} \\boldsymbol{x} = \\boldsymbol{G}(\\boldsymbol{x})$$\n\nwhere $\\boldsymbol{x}$ represents the model state variables, i.e., the marine tracer(s) concentration.\nFor a single tracer, $\\boldsymbol{x}$ can be interpreted as the 3D field of its concentration.\nIn AIBECS, $\\boldsymbol{x}$ is represented as a column vector (that's why it's **bold** and *italic*).\n\nThe operator $\\mathbf{T}$ is a spatial differential operator that represents the transport of tracers.\nFor example, for a single tracer transported by ocean circulation,\n\n$$\\mathbf{T} = \\nabla \\cdot(\\boldsymbol{u} - \\mathbf{K}\\nabla)$$\n\nrepresents the effects of advection and eddy-diffusion\n(where $\\boldsymbol{u}$ is the 3D vector of the marine currents and $\\mathbf{K}$ is a 3×3 eddy-diffusivity matrix).\nThus, $\\mathbf{T}$ \"acts\" on $\\boldsymbol{x}$ such that $\\mathbf{T}\\boldsymbol{x}$ is the flux divergence of that tracer.\nIn AIBECS, $\\mathbf{T}$ is represented by a matrix (that's why it's **bold** and upstraight).\n\nLastly, 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) $\\boldsymbol{x}$.\n\nTo simulate tracers using the AIBECS, you just need to define the transport operators $\\mathbf{T}$ and the net sources and sinks $\\boldsymbol{G}$.\nThat's pretty much the whole concept!\n\n## Note on maintenance and development\n\nNote that AIBECS is essentially in maintenance-only mode, and might remain so for a little while.\nAlthough 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.\nPlease get in touch if you have some bandwidth and/or funding and are interested in collaborating or developing AIBECS!\n\n## References\n\nThis code is © Benoît Pasquier (2024) and contributors, and it is made available under the MIT license enclosed with the software.\n\nOver 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.\nThis can be to this code directly,\n\n\u003e 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](https://doi.org/10.5281/zenodo.2864051).\n\nor to the paper that describes it,\n\n\u003e  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](https://doi.org/10.21105/joss.03814)\n\nor (ideally) both.\nYou can also find the citation(s) in BibTeX format in the [CITATION.bib](./CITATION.bib) file.\n\nIf you use data provided by this package (like the ocean circulation from the OCIM), please cite them as well.\n\nAlso, 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](www.bpasquier.com)), I would be happy to contribute and collaborate!\n\n\u003cimg src=\"https://www.nsf.gov/images/logos/NSF_4-Color_bitmap_Logo.png\" alt=\"NSF\" title=\"NSF_logo\" align=\"right\" height=\"50\"/\u003e\n\nThe authors acknowledge funding from the Department of Energy grant DE-SC0016539 and from the National Science Foundation grant 1658380.\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.21105/joss.03814","https://doi.org/10.5281/zenodo.2864051"],"works":{"https://doi.org/10.21105/joss.03814":{"id":"https://openalex.org/W4206207172","doi":"https://doi.org/10.21105/joss.03814","title":"AIBECS.jl: A tool for exploring global marine biogeochemical cycles.","display_name":"AIBECS.jl: A tool for exploring global marine biogeochemical cycles.","publication_year":2022,"publication_date":"2022-01-05","ids":{"openalex":"https://openalex.org/W4206207172","doi":"https://doi.org/10.21105/joss.03814"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.03814","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.03814.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"Journal of open source software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://joss.theoj.org/papers/10.21105/joss.03814.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075683232","display_name":"Benoît Pasquier","orcid":"https://orcid.org/0000-0002-3838-5976"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Benoît Pasquier","raw_affiliation_string":"","raw_affiliation_strings":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088078785","display_name":"François Primeau","orcid":"https://orcid.org/0000-0001-7452-9415"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"François Primeau","raw_affiliation_string":"","raw_affiliation_strings":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5086338428","display_name":"Seth G. 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