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Peter Cooper, Ph.D., from the National Center for Biotechnology Information (NCBI) will be remotely leading this experimental workshop on how to use EDirect to access NCBI's databases. The VCU community and the general public are welcome to register for this workshop. Registration is required to attend.

The EDirect suite of programs allows easy command line access for searching and retrieving literature (PubMed) and accessing NCBI's biomolecular (Gene, Nucleotide, sequence databases, etc.) records. Its advantages include direct command-line access to NCBI's databases without writing Perl or Python scripts, construction of custom pipelines for processing data, built-in batch access, and the ability to generate highly flexible custom output reports.

Schedule on Tuesday, July 26, 2016

9 a.m.: Overview of Unix/Linux command line basics
10 a.m. - 12 p.m.: EDirect

During the first hour of this workshop, you will learn some basic knowledge about how to use the Unix/Linux command line interface. The second part of the workshop will cover how to use EDirect to set-up simple pipelines to retrieve and process data from PubMed, Gene, and the Nucleotide and Protein sequence databases. Access to EDirect installed in a Linux environment on a cloud service will be provided. Registrants who are already familiar with Unix/Linux are free to join us later at 10 a.m. to learn about EDirect.


Please bring your own laptop. If you have a Windows laptop, you will need to install an SSH Client such as PuTTY (exe file only); Macs should already include a Terminal application. If you need to borrow a laptop for this workshop, please send an email to gaukh@vcu.edu prior to the event. Loaner laptops are available in a limited quantity and must be requested beforehand.

About Peter Cooper, Ph.D.

Peter Cooper, Ph.D. is a Staff Scientist at the National Library of Medicine. Peter has directed the NCBI scientific education and outreach efforts for the past 18 years. He also provides user support for the NCBI molecular databases and the BLAST sequence similarity search services and contributes to feature and interface design for the BLAST standalone and web services.

More Information

If special accommodations are needed, or to register offline, please call 804.628.2291 prior to Thursday, July 21, 2016. Please contact gaukh@vcu.edu if you have any questions about this event. 

This workshop is co-sponsored by VCU Libraries and the VCU Wright Center for Clinical and Translational Research. Virginia Commonwealth University is an equal opportunity/affirmative action employer.

Tuesday, July 26, 2016
9:00am - 12:00pm
Registration has closed.

Event Organizer

Profile photo of Karen Gau
Karen Gau