A Librarian's Guide to NCBI

A workshop for librarians on NCBI tools and resources consisting of an online pre-course and a five-day in-person course held at the National Library of Medicine.

Course Overview

Health science librarians are invited to participate in a new bioinformatics training course, A Librarian’s Guide to NCBI, sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine NLM Training Center (NTC). The course provides basic knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Participating in this course will improve your ability to initiate or extend bioinformatics services at your institution. Prior knowledge of molecular biology and genetics is not required.

Online and In-person Course Components

There are two parts to A Librarian’s Guide to NCBI, listed below. Applicants must take both parts.

Part 1: Fundamentals in Bioinformatics and Searching, a three-week, online, (asynchronous) self-paced pre-course, March 4-25, 2013.

Part 2: A subsequent 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland, April 15-19, 2013.

The format of both components of the course is a combination of instruction, demonstration, discussions, and hands-on exercises (both individual and group). The online component also makes use of videos and readings.

The course description, below, has more detailed information.

Instructors

Instructors will be NCBI staff and Diane Rein, Ph.D., M.L.S., Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo.

CE Credits

MLA CE credits will be available. Currently pending approval.

Who can apply?

• Applications are open to health science librarians in the United States.
• Applicants will be accepted both from libraries currently providing bioinformatics services as well as from those desiring to implement services.
• Enrollment is limited to 18 participants

What does it cost?

• There is no charge for the class. Travel and lodging costs are your responsibility.

How to apply

Please fill out the on-line application form. You will also need to submit your CV and a support statement from your institution. The application form has detailed instructions.

Important Dates

• Application deadline: January 25, 2013
• Acceptance notification: February 15, 2013

Course Description and Preliminary Schedule

Part 1: Fundamentals in Bioinformatics and Searching (asynchronous online)

The purpose of the pre-course is to provide, from a librarian’s professional perspective, the fundamental knowledge and background information needed for the subsequent, more intensive, hands-on second portion of the course onsite at NLM. The course will introduce bioinformatics both as a discipline and as a research practice and preview select NCBI databases, tools (including search tools), and records. The pre-course will also develop the necessary molecular biology vocabulary to enable successful NCBI searches.

Part 2: 5-day in-person course offered on-site at the National Library of Medicine

The in-person course will focus on using the BLAST sequence similarity search and Entrez text search systems to find relevant molecular data. This portion of the Librarian’s Guide to NCBI will describe the various kinds of molecular data available, and explain how these are generated and used in modern biomedical research. A brief schedule and topical outline are provided below.

Schedule of Topics for the Librarian's Guide

Current Agenda

• Monday, April 15

  • Morning Session: Molecular Biology Basics. Gene as a central biological concept and a central NCBI database. (Slides, Exercises)
    • NCBI Resources: Gene, HomoloGene, Nucleotide, Protein, Structure, Graphical Sequence Viewer, Cn3D
  • Afternoon Session: Using Entrez fielded searches, links, and neighbors to find molecular data. (Slides)
    • NCBI Resources: Gene, Nucleotide, Protein, PubMed, PMC, BLink, MyNCBI

• Tuesday, April 16

  • Morning and Afternoon Sessions: Sequence similarity searching using NCBI BLAST. (Slides)
    • NCBI Resources: NCBI BLAST services, Sequence Databases

• Wednesday, April 17

  • Morning Session: Understanding DNA and RNA sequences, assemblies, and genomes. (Slides, Exercises)
    • NCBI Resources: Assembly, BioProject, Gene, Genome, Nucleotide
  • Afternoon Session: Sequence variation and its consequences. (Slides, Exercises)
  • • NCBI Resources: ClinVar, dbGaP, dbSNP, dbVAR, Genetic Testing Registry, Graphical Sequence Viewer, MedGen, PheGenI, Variation Viewer

• Thursday, April 18

  • Morning Session: Gene expression and biological pathways at NCBI. (Slides, Exercises)
    • NCBI Resources: BioSystems, EpiGenomics, Gene, GEO Databases (Datasets, Profiles), UniGene
  • Afternoon Session: Protein structure and function. (Slides, Exercises)
    • NCBI Resources: Protein, Structure, Conserved Domains, CDD Search, Cn3D Viewer

• Friday, April 19

  • Morning Session: Drugs and other small bioactive molecules. (Slides, Exercises)
    • NCBI Resources: PubChem Databases (Substance, Compound, BioAssay)
  • Afternoon Session: Special topics, NCBI/NLM tours, and NCBI Forum.

Contact

Please write to ncbi_course@utah.edu with any questions.