Programmatic access to data resources

Trainers: Nandana Madhusoodanan, Fabio Madeira

Overview: This session will introduce the concept of programmatic access, specifically using REST APIs. You’ll learn how to use EMBL-EBI’s biological data and tools in an automated way,  by writing scripts instead of doing everything manually through a website. We will cover the basic ideas behind APIs—how they work, how to send requests and get results—and prepare you to use them with different EMBL-EBI resources.

Learning outcomes

By the end of this session, you will be able to:

• Explain how REST APIs function and how they enable automated access to biological data and tools
• Apply the basic principles of programmatic access using REST APIs to retrieve biological data from EMBL-EBI resources through scripting.

Materials

• Introductory lecture
• Practical: Programmatic access to data resources
• Practical: BLAST workflow

Please note that the practical materials will redirect you to a Google Colab file.

Never used Google Colab before?

Google Colab is a free cloud-based service that allows you to write and execute Python code in your web browser, similar to what Google Docs allows for writing. To run and modify the code provided here, you can:

• Download the Colab file as a .ipynb file, and open it with Jupyter Notebook. You can then work on the code on your own machine. Please note that by doing so, you will have to independently manage the code dependencies.
• Create your own private copy of the Colab in your Drive

You can also find more information on Jupyter notebook and how to install it in the “Installing Jupyter” page of their website. Note however that by running the practicals on your own machine you may have to independently manage the code dependencies.