NCBI logo

"A Librarian's Guide to NCBI" Course was a Success!

Monday, April 29, 2013

"A Librarian's Guide to NCBI" Course was a Success!

Monday, April 29, 2013

Last week (April 15-19, 2013), NCBI in collaboration with the National Library of Medicine and the National Network of Libraries of Medicine NLM Training Center at the University of Utah presented "A Librarian’s Guide to NCBI". This new course, which was highly rated by participants, was designed to prepare health science librarians for supporting and training patrons about NCBI molecular databases and tools at their own institutions.

As promised in last week’s NCBI Insights Blog post, the materials used in "A Librarian's Guide to NCBI" are now available for download and use for personal enlightenment or to supplement training in workshops or courses. 

On a typical day the course offered two modules, each one focused on a different aspect of molecular data at NCBI and included a short lecture followed by an assessment quiz, instructor-led practical demonstrations, and individual practice problems. In addition to the modules, there were two discussion sessions reviewing library patron questions provided by participants, an open question and answer session with NCBI engineering branch supervisors, a tour of the National Library of Medicine, and a visit by NCBI Director David Lipman. An online forum for the librarian cohort is being developed for continued communications and support.

Participants, instructors, and organizers in the first offering of “A Librarian’s Guide to NCBI” outside the National Library of Medicine including librarians from 21 universities, medical centers and research institutions representing 14 states. Instructors were NCBI Staff Members Peter Cooper, Bonnie Maidak, Wayne Matten, Majda Valjavec-Gratian, Eric Sayers and Rana Morris, as well as Diane Rein from the University at Buffalo.

Based on strong participant evaluations and requests, we are planning to offer the Librarian’s Guide at least once a year.

Check back on NCBI’s Education page for future offerings of this and other NCBI courses.


In addition to their usage in "A Librarian's Guide to NCBI", the curricular materials were developed as separate stand-alone modules to be used by educators and bioinformatics trainers. These are now available for download on the Librarian Course FTP site.

Modules were developed to explain and demonstrate related NCBI resources for use by researchers of broad biology-based disciplines. In each of the eight modules the following questions were answered:

  • Why are the data generated?
  • How are the data generated / determined / measured? 
  • How does the NCBI organize and represent the data? 
  • What tools are available at the NCBI to analyze / search the data? 
  • What experimental questions can be answered with the data?
  • What are the caveats / limits of data interpretation? 
  • What would library patrons want to do with the data? 

Each module featured a 30-minute lecture followed by a brief assessment quiz with a discussion of the answers, instructor-led practical demonstrations, and individual practice problems, and topics covered were:

NCBI Librarian Course Slide Examples

Sample slides from the eight modules of A Librarian’s Guide to NCBI. Complete PowerPoint files are available from the Librarian Course FTP site.

  • Molecular Biology Basics - a review of molecular biology concepts focusing on biological information flow and the gene as a central theme and showed how the NCBI Gene database serves as a central access point for molecular data at NCBI.
  • Advanced Entrez Searchinga demonstration of how to use the Entrez integrated database and search system to find relevant data using both basic and advanced interfaces and fielded searches. The module also demonstrated the importance of pre-compiled and pre-computed relationships for navigating within a database and laterally across the Entrez system.
  • NCBI BLAST a full-day introduction to sequence similarity searching using NCBI’s Basic Local Alignment Search Tool (BLAST). This module covered the basics of sequence alignment algorithms, scoring matrices, and local alignment statistics and used practical protein and nucleotide search examples that highlighted features of the BLAST web service designed to give the most relevant results.
  • Sequences & Genomes - an exploration of the essential role of nucleotide and protein sequence data in modern biological research and the Nucleotide database as the backbone of the NCBI molecular databases. The module explained how NCBI manages and processes sequence and other data associated with genomes and their annotation. Demonstrations and exercises showed how to identify the most up-to-date and well-annotated sequence.
  • Sequence Variation and its Consequences - an examination of the many databases and tools at NCBI that provide access to variation data emphasizing the association between variation and disease risk. After describing the different types of genetic variation as well as the major study methods that produce these data, practical demonstrations and exercises demonstrated how to navigate the NCBI variation resources to find specific data and important attributes, such as geographic population, allele frequency, and disease association.
  • Gene Expression & Biological Pathways - a review of NCBI databases and tools relevant to the study of gene expression. The module provided basic background on the importance of gene expression in various biological phenomena and high-throughput techniques for measuring expression. Practical demonstrations showed how to find and compare expression patterns of genes in different samples in microarray datasets and expression profiles, and how to map selected genes onto metabolic pathways.
  • Protein Structures - an illustation of the usefulness and interconnectedness of NCBI protein structure databases and tools using the example DNA Topoisomerase II. The module covered basic concepts of structural biology and the importance of 3D structure information in understanding the normal functions of proteins and abnormal functions that result in disease. Practical examples showed how to find available 3D structural data for a given protein sequence, detect functional domains within the sequence, view 3D structure data using Cn3D, and explore the relationship between protein sequence and structure data.
  • Drugs & Other Small Molecules - a tour of NCBI’s Chemical and Bioactivity Databases developed by The PubChem Project. The module explained and explored the data in and relationship between PubChem databases (Compound, Substance and BioAssay). Practical examples elucidated the types of data that are accessible from these resources, and provided case-study specific, guided demonstrations for finding information to answer important scientific questions.

Based on course feedback, we plan to expand the course materials to include a set of videos of the lectures and demonstrations to be produced for the NCBI YouTube Channel as well as a set of worked exercises suitable for classroom teaching.

Visit NCBI’s Education page for links to these and other training materials.


  • Jan
  • Feb
  • Mar
  • Apr
  • May
  • Jun
  • Jul
  • Aug
  • Sep
  • Oct
  • Nov
  • Dec

Archives prior to July, 2012

Write to the Help Desk