AWS SageMaker for Bioinformatics

written by Samantha Langit

The Bioinformatics Research Challenge

As a college student who needs to hand in bioinformatics homework, I considered trying out AWS SageMaker to run a Jupyter notebook as it allows me to share my work and make it reproducible for others.

AWS SageMaker

As mentioned, SageMaker provides scalable cloud hosting for Jupyter notebooks.

Cloud-hosted Jupyter notebook

Here are the steps I took:

  1. Test: When the notebook environment was ready, I opened and tested the instance to see if it would run as expected. To do this, I picked a sample notebook from the given list, ‘trusted’ that sample within the notebook environment, and used shift+enter to run a cell. With that successful, I could shutdown that sample notebook.
  2. Customize: I then made a new folder at the root level and named it (for the existing notebook relating to my specific use case). I uploaded the relevant Jupyter notebook into it, then ran it in the same way as I did with the sample notebook. I can, of course, change any values or add any additional code for further analysis.

Summary and Next Steps

Cloud Architect who codes, Angel Investor