A Librarian's Guide to NCBI

A Librarian's Guide to NCBI is a course for librarians on NCBI tools and resources . The course consists of an online portion, Fundamentals of Bioinformatics and Searching, and a 5-day in-person course held at the National Institutes of Health that builds on the knowledge and skills provided by the online class.

Course Overview

Health science librarians are invited to participate in a rigorous 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 knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI.  Prior knowledge of molecular biology and genetics is not required.  Participating in a Librarian's Guide will improve your ability to initiate or extend bioinformatics services at your institution.

Online Pre-Course and In-Person Course Components

There are two parts to A Librarians Guide to NCBI, listed below.  Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2).

  • Part 1:  Fundamentals in Bioinformatics and Searching (online, asynchronous) October 26 – December 11, 2015

This course is offered online (asynchronous) from October 26 – December 11, 2015. The major goal of this course is to provide an introduction to bioinformatics theory and practice in support of developing and implementing library-based bioinformatics products and services. This material is essential for decision-making and implementation of these programs, particularly instructional and reference services. The course encompasses visualizing bioinformatics end-user practice.  It places a strong emphasis on hands-on acquisition of NCBI search competencies and developing a working molecular biology vocabulary through self-paced hands-on exercises.

  • Part 2:  A 5-day class at the National Library of Medicine in Bethesda, Maryland (in-person) March 7 – 11, 2016.

The in-person course will focus on using the BLAST sequence similarity search and Entrez text search systems to find relevant molecular data. The course will describe the various kinds of molecular data available, and explain how these are generated and used in modern biomedical research.  The course will be a combination of instruction, demonstration, discussions, and hands-on exercises (both individual and group)

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

Students successfully completing the Fundamentals course (Part 1) will earn 18 MLA CE credits. Those successfully completing the 5-day in-person class (Part 2) will earn 36 additional MLA CE credits.

Who can apply?

  • Applications are open to health science and basic 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 30 participants.

What does it cost?

  • There is no charge for the classes. Participants are responsible for their own travel, lodging and related costs for the in-person portion.

Applying to the Course

Applications now closed.

Librarian's Guide On-site Course information

Location: The Mary Woodard Lasker Center for Health Research and Education (Building 60, Room 134)

Modules and Other Components

  • Biology Basics 
  • Sequences, Assemblies and Genomes 
  • Using NCBI BLAST
  • Libriarian's Guide Graduate Forum
  • Gene Expression and Biological Pathways
  • Biomolecular Structure and Function
  • Patron Question Practice
  • Variation
  • Clinical Support Resources
  • Drugs and Other Small Molecules

Group projects

Participants will work in groups of 3 to 4 members. Each group will work together to produce a report on an assigned human gene. NCBI staff will provide a list of human genes and assign one at random to each student group.  On Friday afternoon, each group will report on strategies they used and results that they found when trying to gather information about the assigned gene.

Schedule

Monday, March 7: Molecular Basics and Genes and Introduction to course project

Morning: Molecular Basics and the NCBI Gene Database; Gene Project Overview (Peter Cooper)

Time

Content

08:30am – 09:00am Computer set-up

09:00am09:15am

Overall/Intro/Course Objectives/Agenda

09:15am09:30am

Participant Introductions

09:30am10:00am

Presentation: “Biology Essentials: The Gene Concept, Taxonomy, Homology”

09:45am 10:45am

Hands on: Using the NCBI Gene Database to find molecular data.

10:45am11:00am

Break

11:00am12:00pm               

Gene Project Quick Start

12:00pm01:00pm

Lunch

Afternoon: Genomes and Assemblies  (Bonnie Maidak)

Time

Content

01:00pm1:30pm

Presentation: “Sequence Data and Genome Assemblies at NCBI””

01:30pm02:30pm

Instructor-led and independent practice: Finding, displaying, and working with sequence data. and genome

02:30pm02:45pm

Break

02:45pm04:00 pm

Gene project independent group work

 Patron Questions / Discussion

04:00pm05:00pm

Patron Questions / Group Discussion

Tuesday, March 8: Structure; BLAST part 1, protein BLAST

Morning: Biomolecular Structure and Function  (Eric Sayers)

Time

Content

09:00am09:30am

Presentation: “Protein Structure: concepts, experimental techniques, databases and tools at the NCBI”

09:30am10:30am

Instructor-led and independent practice : Finding and displaying protein structures and alignments in the Structure database and with Cn3D

10:30am10:45am

Break

10:45am12:00pm

Gene project independent group work

12:00pm01:00pm

Lunch

Afternoon:  Using NCBI BLAST part 1 (Diane Rein)

Time

Content

01:00pm2:30pm

Presentation: “How BLAST Works”: Theory to Practice Exercise 1; Question and Answers

02:30pm02:45pm

Break

02:45pm03:15pm

Protein BLAST: The Interface: Theory to Practice Exercise 2

03:15PM – 03:30pm Saving BLAST Results
03:30pm – 5:00pm Protein BLAST: Sorting/limiting/editing/results

Wednesday, March 9: NCBI BLAST part 2; Gene Expression and Pathways

Morning: Using NCBI BLAST part 2 (Diane Rein, Peter Cooper)

Time

Content

08:30 am9:00am

Protein BLAST: Determining sequence Function

09:00am-10:00am Gene project independent group work
10:00am-11:00am Nucleotide BLAST + exercise: Theory to Practice Exercise 3
11:00am – 11:15am Break
11:15am 12:00 pm Other alignment services (COBALT, Primer-BLAST, SmartBLAST, MOLE-BLAST) (Peter Cooper)

12:00pm 01:00pm

Lunch

Afternoon: Gene Expression  (Majda Valjavec-Gratian)

Time

Content

01:00pm01:30pm

Presentation: “Gene expression background and working with data in GEO, EpiGenomics, BioSystems and UniGene ”

01:30pm12:30am

Instructor-led and independent practice: Comparing relative expression using GEO, EpiGenomics, BioSystems, and UniGene

02:30pm – 02:45pm

Break

02:45pm04:00pm

Gene project independent group work

Librarian's Guide Graduate Forum

Time

Content

04:00pm – 05:00pm

Presentations and Q&A with Lib. Guide graduates

Thursday, March 10: Sequence Variation; Clinical Support Resources

Morning:  Sequence Variation -- dbSNP, dbVar, 1000Genomes, dbGaP (Wayne Matten)

Time

Content

09:00am09:30am

Presentation: “Sequence Variation in dbSNP, dbVar, 1000Genomes, dbGaP, ClinVar”

09:30am10:30am

Instructor-led and independent practice :  Exploring sequence variations at NCBI

10:30am10:45am

Break

10:45amNoon

Gene project independent group work

12:00pm01:00pm

Lunch

Afternoon: Clinical Support Resources (Rana Morris)

Time

Content

01:00pm1:30pm

Presentation: "Clinical Support Resources at NCBI" (MedGen, GeneReviews, GTR, ClinVar, ClinicalTrials.gov)

01:30pm02:30pm

Instructor-led and independent practice :  Finding Relevant Information about Diseases/Conditions

02:30pm02:45pm

Break

02:45pm04:00pm

Gene project independent group work

Patron Questions / Discussion (All Instructors)

Time

Content

04:00pm5:00pm

Patron questions / Group Discussion

Friday, March 11: Drugs and Other Small Molecules, NLM Tour, Gene Reports

Morning: Drugs and Other Small Molecules  (Rana Morris)

Time

Content

09:00am09:30am

Presentation: “NCBI’s PubChem: Compound and BioAssay"

09:30am10:30am

Instructor-led and independent practice: Finding chemical information and biological activity for drugs and other small molecules

10:30am10:45am

Break

10:45am12:00pm

Gene project independent group work

12:00pm02:00pm

Lunch and NLM Tour (Tour begins at 12:30. Lasts about 1 hour.)

Afternoon: Group presentations

Time

Content

02:00pm2:30pm

NCBI APIs and programmatic access

02:30pm 04:30pm

Group preliminary gene presentations

04:30pm05:00pm

Overall course wrap-up and evaluation

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

Support Center

Last updated: 2016-03-03T10:40:41-05:00