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Accessing NCBI Biology Resources Using EDirect for Command Line Novices

This workshop will be held on July 18th, 2023. 

NCBI Faculty:  E. Sally Chang, PhD

Workshop Duration: 2 hours

Content Difficulty: Beginner

Target Audience:
This workshop is for biological researchers who would like to learn to use the command line for searching and fetching NCBI data. You do not need to have had prior experience with the command line, but we do recommend that you have some familiarity with NCBI databases get the most of this workshop.

Workshop Description:

In this workshop, we will begin with an introduction to working in a command line environment and then show you how to use the EDirect suite to access data programmatically from several NCBI databases.

In this workshop you will learn how to:

  • Write Bash commands with parameters
  • Download and store data files in an organized directory structure
  • Construct search queries using NCBI’s EDirect to search in a specific database, link to related data in another database, and download selected information.
  • Chain together multiple command line calls in a reusable workflow which can quickly and reproducibly access the latest information.

Jupyter notebook button iconThis link goes to an interactive version of the notebook presented in the workshop. Please Note:  that it may take up to 10 minutes to load the first time you access these materials.

Last Reviewed: July 19, 2023