On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.
NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.
You must provide your own laptop with wireless internet capabilities. If you have a Windows laptop, you will need to install the CygWin package yourself before coming to the workshop. In addition to the basic CygWin installation, you will also need to install the Perl package and the unzip and nano programs. These are both available from the CygWin site. Mac laptops should need no additional software installed except the EDirect package itself. We will install EDirect as part of the workshop.
During the optional first hour of this workshop (9 – 10 AM), you will get a basic introduction to the Unix/Linux command line interface. The main workshop (10 AM – Noon) 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.
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.