SBMI - AI4metabolomics

Analyzing an organism's metabolism is crucial for understanding and monitoring diseases and treatments. Magnetic resonance imaging (MRI) is the only technique to measure the metabolism noninvasively, in vivo, and in vitro.

With this application you can detect and measure the abundance of prespecified substances of NMR spectra.

Run the App

Notes

This app is not a fully debugged application. Some cases may lead to bugs. These bugs should not apply to the fitting process itself. If you run into an error, please restart the app. It is important to quit the app via the terminal by pressing CTRL + C.

It is recommended to use python version >= 3.10 for this application.

Install Git

To use git, please install it with following this link.

Download the GitHub repository

1. Download this directory and put it into a place on your system where you like. You can download the directory using either git:

git clone --depth 1 https://github.com/RATFIVE/SBMI-AI4metabolomics.git

or download the directory from the github repository by

1. open this link: https://github.com/RATFIVE/SBMI-AI4metabolomics,
2. press on the green code button and 
3. 'Download ZIP'. Depending on your internet speed it will take a certain time because of past development code.

Install Virtual Envirnoment

You can install all the libaries in a seperate python enviroment.

1. Go into the app directory:

cd path_of_your_download_dir\SBMI-AI4metabolomics-main\app

2. Create a Virtual Environment in the app dir:

python -m venv .SBMI

3. Activate the Virtual Environment

.SBMI\Scripts\activate

4. Use this command to install the required python packages

pip install -r requirements.txt

5. Start the app

streamlit run app.py --server.port=8501

The app should open now in the browser

You can always access the app by the url. Paste this in your browser(for example Firefox)

http://localhost:8501

Quit the app

To quit the app go back to the running terminal and press CTRL + C. This is important. If this is not done more and more instances would be created and will eventually fill up the memory(RAM).