Notebook environment for both interactive data analysis and batch data processing

Introductory Videos


Presentation at JupyterCon 18
slides and examples


Overview of SoS Notebook

Getting help

SoS Notebook comes with an extensive set of documentation but it can be daunting to dive into it to get the information you need.

  • If you have a casual question like if certain feature exists or how certain things are handled, it is better to ask it in our gitter channel. You can also use the button at the top right corner of the homepage.

  • If you have a more serious question or suggestion, please feel free to post to our issue tracker. SoS consists of tens of modules and related issue trackers but free feel to post to any of them because it is easy for us to move the issue to an appropriate tracker if needed.


Our documentation is hosted on our live server and can be edited directly. If you spot an error or feel like contributing to the document, please

  1. Click the     button to the top right corner of each tutorial
  2. Execute the notebook and edit it on our live server
  3. Enter !create-pr <Shift-Enter> in the console panel to send us a PR


Jupyter notebook to demonstrate features of SoS


Please cite the following publication if you use SoS Notebook for your work:

SoS Notebook: An Interactive Multi-Language Data Analysis Environment Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James Melott, Yulun Chiu, Di Du, and John N. Weinstein, Bioinformatics, May 2018. doi: