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Development","sub_category":"Education","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# [JuliaCon 2021](https://juliacon.org/2021/) Workshop\n\n**Title:** Modeling Marine Ecosystems At Multiple Scales Using Julia\n\n**Speakers:** [Gael Forget](https://github.com/gaelforget), [Benoit Pasquier](https://github.com/briochemc), [Zhen Wu](https://github.com/zhenwu0728)\n\n## 2021/07/25 Workshop Recording\n\nstreaming : https://www.youtube.com/watch?v=UCIRrXz2ZS0\n\nwebpage : https://pretalx.com/juliacon2021/talk/FEZW9Q/\n\ndocumentation : https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/\n\n[\u003cimg src=\"https://user-images.githubusercontent.com/20276764/132381907-1ab7d682-ea3d-4db7-b245-3cdb9dd2dcd3.png\" width=\"75%\"\u003e](https://www.youtube.com/watch?v=UCIRrXz2ZS0)\n\n## Abstract\n\nLife in the oceans is strongly connected to our climate. In this workshop, you will learn to use packages from the [JuliaOcean](https://github.com/JuliaOcean) and [JuliaClimate](https://github.com/JuliaClimate) organizations that provide a foundation for studying marine ecosystems across a wide range of scales. We will run agent-based models to explore individual microbes and processes that drive species interactions. On the other end of the model hierarchy, we will simulate planetary-scale transports that control ocean biogeography and climate change.\n\n## Notebooks\n\nAny example found in the online documentation is most easily run using [Pluto.jl](https://github.com/fonsp/Pluto.jl) . \n\nJust copy the corresponding `notebook url` link below and paste into the [Pluto.jl interface](https://github.com/fonsp/Pluto.jl/wiki/🔎-Basic-Commands-in-Pluto) (v0.15 or later).\n\n- [AIBECSExample.html](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/AIBECSExample.html) (---\u003e [notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/AIBECSExample.jl))\n- [PlanktonIndividualExample.html](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/PlanktonIndividualExample.html) (---\u003e [notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/PlanktonIndividualExample.jl))\n- [MITgcm_tutorial_global_oce_biogeo.html](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/MITgcm_tutorial_global_oce_biogeo.html) (---\u003e [notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/MITgcm_tutorial_global_oce_biogeo.jl))\n- [IndividualDisplacementsExample.html](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/IndividualDisplacementsExample.html) (---\u003e [notebook url](https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/IndividualDisplacementsExample.jl))\n\n## Description\n\nPackages covered in this workshop include:\n\n- [AIBECS.jl](https://github.com/JuliaOcean/AIBECS.jl): global steady-state biogeochemistry and gridded transport models that run fast for long time scales (centuries or even millennia).\n- [PlanktonIndividuals.jl](https://github.com/JuliaOcean/PlanktonIndividuals.jl): local to global agent-based model, particularly suited to study microbial communities, plankton physiology, and nutrient cycles.\n- [MITgcmTools.jl](https://github.com/gaelforget/MITgcmTools.jl): interface to full-featured, Fortran-based, general circulation model and its output (transports, chemistry, ecology, ocean, sea-ice, atmosphere, and more).\n- [IndividualDisplacements.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl): local to global particle tracking, for simulating dispersion, connectivity, transports in the ocean or atmosphere, etc.\n\nThe workshop was organized around tutorials and self-contained Pluto notebooks for the different packages.\n\n## Schedule\n\n- Introduction of the topics covered, presenters, installation, and workshop roadmap (15 minutes).\n\n- [AIBECS.jl](https://github.com/JuliaOcean/AIBECS.jl): concept, implementation, tutorial workthough (30 minutes + 10' for questions; [this notebook URL](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/AIBECSExample.jl))\n\n- [PlanktonIndividuals.jl](https://github.com/JuliaOcean/PlanktonIndividuals.jl): concept, implementation, tutorial workthough (30 minutes + 10' for questions; [this notebook URL](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/PlanktonIndividualExample.jl))\n\n- [ClimateModels.jl](https://github.com/gaelforget/ClimateModels.jl) and [MITgcmTools.jl](https://github.com/gaelforget/MITgcmTools.jl): concept, implementation, tutorial workthough (20 minutes + 10' for questions; [this notebook URL](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/MITgcm_tutorial_global_oce_biogeo.jl))\n\n- [ClimateModels.jl](https://github.com/gaelforget/ClimateModels.jl) and [IndividualDisplacements.jl](https://github.com/JuliaClimate/IndividualDisplacements.jl): concept, implementation, tutorial workthough (20 minutes + 10' for questions; [this notebook URL](https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/IndividualDisplacementsExample.jl))\n\n- Q\u0026A, tutorials, etc wrap-up\n\nWorkshop materials are available ahead of time @ https://github.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl\n\n\n\n## Setup instructions\n\n\nTo run the notebooks of this workshop on your machine, you need to:\n\n1. **Install Julia** from \u003chttps://julialang.org/\u003e (latest version is v1.6.2)\n\n1. **Start Julia**\n\n1. **Add Pluto.jl** (v0.15.0 or later)**\n\n    This is simply done by typing, in the julia REPL,\n\n    ```julia\n    import Pkg\n    Pkg.add(\"Pluto\")\n    ```\n\n    \u003e *Note*: Please make sure you get version 0.15.0 or later.\n    \u003e If you get an older version then you can add Pluto in a clean, temporary, environment as follows:\n    \u003e ```julia\n    \u003e import Pkg\n    \u003e Pkg.activate(mktempdir())\n    \u003e Pkg.add(\"Pluto\")\n    \u003e ```\n\n1. **Use Pluto to run the notebooks.**\n    This is as simple as copy-pasting one of the following lines, depending on which notebook you want to run:\n\n    ```julia\n    using Pluto\n    Pluto.run(notebook=\"https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/AIBECSExample.jl\")\n    ```\n**Alternatively**, instead of your own computer, you can just launch a Pluto instance in the cloud using [JuliaHub.com](https://juliahub.com/ui/Home), paste a notebook URL in the [Pluto start page](https://github.com/fonsp/Pluto.jl), and click open.\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["tracer","biogeochemistry","ocean","oceanography","ocean-modelling"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/25132","html_url":"https://ost.ecosyste.ms/projects/25132"}