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 - 10:00 Lecture 1 The Four Basic Pipelines 10:00 - 10:15 Break 10:15 - 11:00 Practical 1 Demonstration of ESearch-ESummary 11:00 - 12:00 Practical 2 Coding the Four Basic Pipelines  Session II E-utility Advanced Topics 13:30 - 14:30 Lecture 2 Extending Pipelines with ELink and ESearch 14:30 - 14:45 Break 14:45 - 15:45 Practical 3 Demonstration of an Extended Pipeline 15:45 - 17:00 Practical 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