Skip to content

shuzhao-li-lab/Notebooks-computational-metabolomics

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

11 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

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 The HTML/ folder is no longer updated, as GitHub renders .ipynb now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:

About

Notebooks in computational metabolomics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published