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Notebooks in Computational Metabolomics

Jupyter notebooks covering topics in metabolomics data analysis and computational methods. Free in the 3-Clause BSD License. Ongoing. Contributions are welcome.

Examples are under notebooks/. The HTML/ folder is no longer updated, as GitHub renders .ipynb now

Use Jupyter notebooks via Docker containers

Install Docker

Example on Linux (Ubuntu/Mint), instructed as -

https://docs.docker.com/install/linux/docker-ce/ubuntu/

sudo apt-get install apt-transport-https ca-certificates curl gnupg-agent software-properties-common

shuzhao@X3:~$ curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -

OK

shuzhao@X3:~$ sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable"

shuzhao@X3:~$ sudo apt update

shuzhao@X3:~$ sudo apt-get install docker-ce docker-ce-cli containerd.io

Test Docker

shuzhao@X3:~$ sudo docker run hello-world

Add me to docker group, so I don't have to use sudo to run docker

shuzhao@X3:~$ sudo groupadd docker

shuzhao@X3:~$ sudo usermod -aG docker $USER

shuzhao@X3:~$ newgrp docker

Use data science stack via Docker

instructed as -

https://jupyter-docker-stacks.readthedocs.io/en/latest/

Scipy notebook

This also maps to local directory w/proj_test:

docker run -v /home/shuzhao/w/proj_test:/home/jovyan/p1 -p 8888:8888 jupyter/scipy-notebook

R notebook

docker run -v /home/shuzhao/w/proj_test:/home/jovyan/p1 -p 8888:8888 jupyter/r-notebook

Example notebooks

Additional notebooks:

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