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This is a Julia package for calculating the Muscle Insulin Sensitivity Index (MISI) from glucose and insulin data from an oral glucose tolerance test (OGTT). The code is based on the work and the MATLAB GUI of O’Donovan et al. 1.
Caution
This package is still fully under construction and not all features are implemented yet. The API is not stable and may change drastically in the future. Please use with caution. If you encounter any problems, please contact Shauna O'Donovan or raise an issue.
Here you will find some instructions on how to make sure the code from this repository can run on your computer. In this instruction, we will assume you are installing the latest stable version of Julia, but any other version is installed in a similar way.
The first step is to install the Julia version manager (juliaup), which enables you to have multiple Julia versions installed on your machine. This step is not mandatory for a properly working version of Julia, but it is useful if you are planning to use Julia for your own projects in the future.
Windows:
Note The
wingetcommand may not be available on your machine! In that case, you can download Julia from the Microsoft Store. If your organization prevents use of the Microsoft Store, you can follow the download instructions from https://julialang.org when clickingDownload
Open your favorite terminal, or press Win+R, type cmd in the text bar and press 'run'.
winget install julia -s msstore
Linux & MacOS:
From the command line execute
curl -fsSL https://install.julialang.org | sh
Afterwards, you can restart the terminal environment. You can install a specific version of Julia using
juliaup add <version>
You can list the versions available to you using
juliaup list
We recommend to start with installing the latest stable version, dubbed release by running
juliaup add release
If this is your only Julia version, juliaup will automatically label this as the default version.
Julia was found to work the best using the VSCode IDE, which you can download here. After downloading and installing VSCode, navigate to the VSCode marketplace, which has the following icon:
Type Julia in the search bar and install the Julia Language Support extension.
After installing Julia, you can either fork this repository to your own Github account and download the code from there, or download the code directly from this repository into a Zip-file by selecting Code -> Download ZIP.
Extract the files in this folder and naviage to the folder location in Visual Studio Code interface by selecting 'Open Folder' in the File Tab.
Open the calculate_misi.jl file and edit the INPUT_FILE_NAME and OUTPUT_FILE_NAME variables to match your desired files. Then, run the file by pressing F5 or by clicking on the "Run" button in the top right corner of the editor (red circle).
Important
Make sure your input file is an Excel file that is formatted in the same way as the example file: Sample_Data.xlsx.
Tip
The calculate_misi.jl file automatically installs the necessary packages and activates the right environment for running the MISI calculator.
If you want to manually activate the environment, you can follow the following instructions:
In case a terminal is not open yet, click Terminal->New Terminal from the top bar and execute
julia
To start the Julia REPL.
Then, press ] to change from Julia to the package manager, which is indicated by >julia changing to >pkg. Then, execute:
activate .
Warning Make sure to remember the dot
.at the end of this command.
To activate the workshop environment. Then execute (also from the Pkg terminal)
instantiate
To install all the required packages.
Footnotes
-
O’Donovan, S. D. et al. Improved quantification of muscle insulin sensitivity using oral glucose tolerance test data: the MISI Calculator. Sci Rep 9, 9388 (2019). ↩