How raw milk-based adjunct cultures influence the microbial diversity in cheese

This repository contains the data and code used in the study "How raw milk-based adjunct cultures influence the microbial diversity in cheese" by Dreier et al. (2024). The study investigates the impact of raw milk-based adjunct cultures (NMAC) on the microbial diversity of cheese. The data includes 16S rRNA gene amplicon sequences from cheese samples, as well as metadata and code used for data analysis.

The full data analysis can be viewed as html.

Open the data_analysis.html in the docs folder after cloning the repository:

data_analysis.html

In order to run the Jupyter notebook and/or to download the complete data set, please follow the instructions below.

How to download the data

1. Clone the repository:

git clone https://github.com/biologger/NMAC_data.git

How to run the Jupyter notebook

1. Install Docker Instructions for installing Docker can be found here.

2. Clone the repository:

git clone https://github.com/biologger/NMAC_data.git

3. Change to the directory:

cd NMAC_data

4. Run the docker run command in the terminal:

sudo docker run --rm -u 0 -v $(pwd):/workdir -p 127.0.0.1:8888:8899 --name dataanalysis biologger/nmac_data_analysis:v1.0

5. Open the following url in your browser:

http://localhost:8888/

http://localhost:8888/

You want to build the Docker image yourself?

1. Clone the repository:

git clone https://github.com/biologger/NMAC_data.git

2. Change to the directory:

cd NMAC_data

3. Build the Docker image:

sudo docker build -t nmac_data_analysis -f ./Analysis_ENV/Dockerfile ./Analysis_ENV/

4. Run the docker run command in the terminal:

sudo docker run --rm -u 0 -v $(pwd):/workdir -p 127.0.0.1:8888:8899 --name dataanalysis nmac_data_analysis

5. Open the following url in your browser:

http://localhost:8888/

http://localhost:8888/