JuliaCon 2021 Workshop

Title: Modeling Marine Ecosystems At Multiple Scales Using Julia

Speakers: Gael Forget, Benoit Pasquier, Zhen Wu

2021/07/25 Workshop Recording

streaming : https://www.youtube.com/watch?v=UCIRrXz2ZS0

webpage : https://pretalx.com/juliacon2021/talk/FEZW9Q/

documentation : https://juliaocean.github.io/MarineEcosystemsJuliaCon2021.jl/dev/

Abstract

Life in the oceans is strongly connected to our climate. In this workshop, you will learn to use packages from the JuliaOcean and 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.

Notebooks

Any example found in the online documentation is most easily run using Pluto.jl .

Just copy the corresponding notebook url link below and paste into the Pluto.jl interface (v0.15 or later).

• AIBECSExample.html (---> notebook url)
• PlanktonIndividualExample.html (---> notebook url)
• MITgcm_tutorial_global_oce_biogeo.html (---> notebook url)
• IndividualDisplacementsExample.html (---> notebook url)

Description

Packages covered in this workshop include:

• AIBECS.jl: global steady-state biogeochemistry and gridded transport models that run fast for long time scales (centuries or even millennia).
• PlanktonIndividuals.jl: local to global agent-based model, particularly suited to study microbial communities, plankton physiology, and nutrient cycles.
• MITgcmTools.jl: interface to full-featured, Fortran-based, general circulation model and its output (transports, chemistry, ecology, ocean, sea-ice, atmosphere, and more).
• IndividualDisplacements.jl: local to global particle tracking, for simulating dispersion, connectivity, transports in the ocean or atmosphere, etc.

The workshop was organized around tutorials and self-contained Pluto notebooks for the different packages.

Schedule

• Introduction of the topics covered, presenters, installation, and workshop roadmap (15 minutes).

• AIBECS.jl: concept, implementation, tutorial workthough (30 minutes + 10' for questions; this notebook URL)

• PlanktonIndividuals.jl: concept, implementation, tutorial workthough (30 minutes + 10' for questions; this notebook URL)

• ClimateModels.jl and MITgcmTools.jl: concept, implementation, tutorial workthough (20 minutes + 10' for questions; this notebook URL)

• ClimateModels.jl and IndividualDisplacements.jl: concept, implementation, tutorial workthough (20 minutes + 10' for questions; this notebook URL)

• Q&A, tutorials, etc wrap-up

Workshop materials are available ahead of time @ https://github.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl

Setup instructions

To run the notebooks of this workshop on your machine, you need to:

1. Install Julia from https://julialang.org/ (latest version is v1.6.2)

2. Start Julia

3. Add Pluto.jl (v0.15.0 or later)**

   This is simply done by typing, in the julia REPL,

   import Pkg
   Pkg.add("Pluto")
   

   Note: Please make sure you get version 0.15.0 or later.
   If you get an older version then you can add Pluto in a clean, temporary, environment as follows:

   import Pkg
   Pkg.activate(mktempdir())
   Pkg.add("Pluto")
   

4. Use Pluto to run the notebooks.
   This is as simple as copy-pasting one of the following lines, depending on which notebook you want to run:

   using Pluto
   Pluto.run(notebook="https://raw.githubusercontent.com/JuliaOcean/MarineEcosystemsJuliaCon2021.jl/main/src/AIBECSExample.jl")
   

Alternatively, instead of your own computer, you can just launch a Pluto instance in the cloud using JuliaHub.com, paste a notebook URL in the Pluto start page, and click open.