Minimal Modeling and Simulation

BPHYS workshop, Fall 2022, Eric Rouviere

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Contents

1. notebooks/ contains the jupyter notebooks we will be working through.
2. src/ contains the source code of much of the workshop.

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Installation of software

1. Install Julia

1. Check type of CPU.

2. Download from https://julialang.org/downloads/

3. Install by clicking on the downloaded file and dragging to applications.

4. Add julia to your PATH by adding the following line to the ~/.bash_profile file.

   export PATH="$PATH:/Applications/Julia-1.8.app/Contents/Resources/julia/bin/"

5. In the command line enter source ~/.bash_profile

2. Installing the nessicary Julia packages

1. Start the julia app. This should open up the terminal with julia running.
2. Type ]. This gets you to the package manager
3. Enter add PyPlot, IJulia, LaTeXStrings, BenchmarkTools
4. Press the delete key to go back to julia.
5. Enter using PyPlot, IJulia, LaTeXStrings, BenchmarkTools.
6. Enter jupyterlab() to start Jupyter IDE. When prompted to install conda, agree.

4. Installing git

1. Got to https://git-scm.com/
2. click "Download for XXX" and follow installer instructions.
3. In the terminal, move to a directory where you want to put the repo (e.g. cd ~/Desktop).
4. Enter git clone https://github.com/ericrouviere/BPHYS_workshop_2022.git

To keep your up repo up to date with changes I make, cd into BPHYS_workshop_2022/ and enter git pull