Accessing NCBI Biology Resources Using EDirect for Command Line Novices

About this Class

This workshop is for life scientists, including educators and research students, who would like to learn to use the command line for searching and fetching NCBI data. 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 biological data from several NCBI databases. 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.

In this workshop you will learn how to:

• Write Bash commands with parameters
• Construct search queries using NCBI’s EDirect to search in a specific database
• Download selected data in chosen file formats
• Link to related data in another database
• Combine commands into reproducible workflows

Note:  This workshop is appropriate for both student researchers themselves as well as educators and mentors who want to help their students learn to use these resources.

Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status 2 weeks before the scheduled event.

We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.

Please see our FAQs page for more information and if you still have questions about the NCBI Outreach Events program or this specific workshop, email us at workshops@ncbi.nlm.nih.gov .