Course Information

  PowerScripting
  Summary
  Objectives
  Intended Audience
  Format

Resources

  Entrez Home
  Entrez Tools
  E-utilities
  Perl Constructs
  Perl Documentation

About the instructors

Questions or Comments

 
NCBI QuickScripts

   Course Summary

The National Center for Biotechnology Information (NCBI) presents NCBI QuickScripts, a one-day computer workshop 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. The course is a condensed version of NCBI PowerScripting, a 4-day course taught on the NIH campus in Bethesda, MD.

   Scheduled Courses
Courses in 2008 Previous Courses

   Course Materials
Slides, Scripts and Handouts Session I Exercises
Practical Guide Session II Exercises

   Course Tools
EBench EPipe
EBot E-Utilities Home

   Course Objectives

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

  • Build and execute E-utility search and retrieval URLs across the 35 Entrez databases
  • Implement E-utility pipelines for genomic, proteomic, or microarray analysis
  • Create and download customized datasets
  • Implement batch search, link, and retrieval functions in Entrez

   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.

   Course Format

The course consists of two 3-3.5 hr sessions that will combine lecture, guided demonstrations, and time for independent work. During the course, participants will use a Perl module and a library of sample Perl scripts as starting materials with which to build E-utility applications.

   Course Schedule
 Session I
E-utility Fundamentals
09:00 - 10:00Lecture 1 The Four Basic Pipelines
10:00 - 10:15Break
10:15 - 11:00Practical 1 Demonstration of ESearch-ESummary
11:00 - 12:00Practical 2 Coding the Four Basic Pipelines

 Session II
E-utility Advanced Topics
13:30 - 14:30Lecture 2 Extending Pipelines with ELink and ESearch
14:30 - 14:45Break
14:45 - 15:45Practical 3 Demonstration of an Extended Pipeline
15:45 - 17:00Practical 4 Coding Extended Pipelines


   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 January 15, 2008

Questions or Comments?
Write to Eric Sayers