Course Information

  Summary
  Objectives
  Intended Audience
  Format
  Venue
  Course Schedule

Resources

  Entrez Home
  Entrez Tools
  E-utilities

Local Information

  NIH
  Bethesda
  Bethesda Hotels
  Montgomery County

Course Materials

  Practical Guide
  Handouts
  Slides
  Scripts
  E-Bench
  E-Pipe
  Ebot
  Perl Constructs
  QuickScripts

About the instructors

Questions or Comments

 
NCBI PowerScripting

   Course Summary

The National Center for Biotechnology Information (NCBI) presents NCBI PowerScripting, a 4-day course including both lectures and computer workshops on effectively using the NCBI Entrez Programming Utilities (E-utilities) within scripts to automate search and retrieval operations across the entire suite of Entrez databases.

Location: Lister Hill Center (Bldg 38A), NLM, NIH, Bethesda, MD

Directions to the National Library of Medicine

   Course Objectives

During the course, participants will learn how to do the following:

  • Post E-utility calls using standard URLs in Perl and using SOAP in Visual C#
  • Design and execute complex searches across the 35 Entrez databases
  • Implement data pipelines for genomic, proteomic, or microarray analysis
  • Create automated searches to keep local databases current
  • Create and download customized datasets
  • Seamlessly combine local data with NCBI data
  • Develop a focused interface to NCBI data

   Intended Audience

The course is intended for bioinformatics and information specialists who are interested in accessing NCBI data in an automated fashion. A working knowledge of NCBI resources and the Perl scripting language is required. No knowledge of SOAP or C# is assumed.

   Course Format

The course consists of a series of lectures and associated computer workshops over 3 days, followed by a morning of discussions, an NCBI tour and an optional afternoon session for individual consultations. Participants will program using Perl 5.8 and Visual Studio C# on Windows XP laptops. NCBI will provide all necessary hardware and software.

Click here to view the course schedule

   Venue

 
The course will be held at the NCBI Training Center in the Lister Hill Center (Building 38A) of the National Library of Medicine on the main NIH campus in Bethesda, MD.
Participants will be responsible for their own transportation, lodging and meals, and there are numerous hotels in Bethesda, as well as in Rockville and surrounding areas of Montgomery County. Bethesda also contains a renowned variety of restaurants that are only a few minutes walk from campus.
Public transportation to the Medical Center Metro stop (Red Line) provides the most convenient access to NIH. See the Local Information links on the left bar of this page for more information.

   About the Instructors

Steve Pechous, Eric Sayers and Tao Tao are biologists on the User Services staff of the National Center for Biotechnology Information.

Revised February 28, 2008

Questions or Comments?
Write to Eric Sayers