The following sections of this review will focus on six categories of educational materials and services for NCBI users: Getting Started, Documentation, Teaching Resources, Courses and Workshops, News and Updates and Community. These six categories also appear on the NCBI Education page, depicted in , which serves as the principal starting point for exploring NCBI educational materials.
The NCBI Education page is the main portal for access to NCBI educational resources.
The Getting Started section contains introductory material designed to orient new visitors to the NCBI site. ‘About NCBI’ is particularly helpful as an introduction to the NCBI site for new users and provides general information about the history, mission and organization of NCBI. In addition, ‘About NCBI’ offers descriptions of the science behind much of the data at NCBI, including introductions to the specialized techniques that generate modern sequence, genome, variation and expression data, all written for people unfamiliar with these methods. Other sections of ‘About NCBI’ explore the nature of whole-genome assemblies and associated data for human and model organism genomes, focusing on understanding how genome data explain human biology and the origins of genetic diseases. Also included in the Getting Started section are the NCBI Resource list and How-to guides from the NCBI Guide.
The last major resource under Getting Started is The NCBI Handbook. This NCBI textbook provides detailed background information on most of the NCBI databases and tools—how they are constructed, what data are in them and how to search them. The book provides a valuable introduction to the NCBI site along with its architecture and culture. The book is organized into three main parts: The Databases, Dataflow and Processing, and Querying and Linking the Data. The Handbook also has a recently updated NCBI glossary that is extensively linked from many parts of the web site and offers definitions of NCBI-specific terminology as well as some general bioinformatics, molecular biology and biochemical terms.
The Documentation section collects basic help documents that provide detailed information about the purpose, function and user-adjustable features of a particular tool or service, as well as practical aspects of its use and special techniques (tips and tricks). NCBI Documentation linked to the Education page encompasses the Resource-specific Help pages and Frequently Asked Questions (FAQs) associated with the various databases and tools as well as NCBI Fact Sheets on these resources.
The Resource-specific Help and FAQ pages gather together in one place all of the available documentation and FAQs that are also linked to the homepages for the specific resources. For example, help documentation for Entrez is closely associated with the database homepages; either linked on the blue sidebar in database homepages with older styles (e.g. www.ncbi.nlm.nih.gov/gene/
) or, in pages with newer styles (e.g. www.ncbi.nlm.nih.gov/ pubmed/
), in the first column of links with information about using the resource. All resource homepages at NCBI are in the process of moving to this newer style, which includes the NCBI search bar and footer area that is also present on the Guide page. The new footer provides rapid navigation to all major areas of the NCBI site and easier navigation to general help documents such as the NCBI Handbook and Help Manual collection by listing them in the ‘Getting Started’ column on the left-hand side.
NCBI Fact Sheets are two- or four-page full-color handouts available in PDF format that describe a specific resource and highlight important features and aspects of its use. The growing collection of fact sheets now includes documents for BLAST, Align 2 Sequences, Primer-BLAST, Books, the Conserved Domain Database, Epigenomics, GenBank, Gene, Map Viewer, the new PubMed design and Variation data (dbSNP). These useful introductions to specific NCBI resources are part of the materials available at the NCBI exhibit booth at scientific meetings described below in the section on Courses and Workshops. These documents can also be downloaded and printed out from the Fact Sheets page linked to Documentation.
The repository and source for much of the resource-specific help is the NCBI Help Manual collection on the Bookshelf, which is also linked separately under Documentation. The NCBI Help Manual collection is a growing set of online books that serve as the major documentation for a particular resource, tool or database. Both the NCBI Handbook and the Help Manual are also linked to the Getting Started section in the NCBI footer that appears on all of the new NCBI pages.
Teaching Resources are instructional materials that demonstrate NCBI tools and databases using specific examples that highlight useful features. These are divided into Tutorials, Educational Tools and the Course Archive. Each category leads to a separate page with additional links. The NCBI Glossary is also linked to the Teaching Resources and provides an up-to-date view of technical terms associated with modern molecular biology, genetics, genomics as well as NCBI-specific terms.
The Tutorials are step-by-step resource- or problem-oriented documents, Web pages or videos that explain how to use a resource or perform a task. Web Tutorials are NCBI Web pages or chapters from the Bookshelf. Some of these show how to use a specific resource, such as the Genome Workbench tutorial. Others, such as the Disease Genes book chapter, follow a path or tell a scientific story that highlights specific tools and databases. The Disease Genes chapter [3
], the BLAST QuickStart chapter [4
] and the 3D structures Web pages are based on the NCBI Mini-courses, one of several previous NCBI instructor-led course offerings. The Problem Sets are additional material from NCBI courses and are printable standalone problem sets or examples. These include the problem sets from the general NCBI Field Guide course and the detailed handouts from the problem-based and resource-oriented NCBI Mini-courses. Although these courses are no longer taught, the materials in Tutorials are maintained so that they work as shown with the current NCBI Web pages and underlying data. Information on current NCBI course offerings is presented below in the Courses and Workshops section. Video Tutorials are short videos and other animated presentations on how to use the NCBI site. Many of these demonstrate aspects of the literature services, PubMed and PubMed Central. In addition there are a growing number of videos such as the ones entitled ‘Downloading records from Entrez’ and ‘Retrieving sequences for an organism’ that are animated renderings of the How-to guides from the NCBI Guide. These show how to perform a specific task in the NCBI molecular databases.
There are also three interactive Educational Tools—originally developed as part of the NCBI training courses—that are useful learning aids. The Amino Acid Explorer displays and sorts amino acids by their physical and chemical properties, shows the consequences of nucleotide mutations and lists the functions of each amino acid in various conserved protein domains. The PSSM Viewer provides insight into important functional elements within proteins through interactive displays of position-specific score matrices (PSSMs) derived either from the NCBI CDD database or produced by standalone PSI-BLAST. The Ebot tool from one of the NCBI technical workshop courses is a demonstration program that translates a user-defined query into a data-gathering pipeline using the Entrez Programming Utilities (E-utilities) interface. The tool generates a downloadable Perl script that can be executed locally to retrieve data.
The NCBI has a long tradition of offering instructor-led workshops. These have included the Mini-courses and Field Guide, computer-oriented technical workshops and the team-taught collaborative course for medical librarians and information specialists. The Course Archive contains these course materials in their original forms and includes the web pages, slide sets and handouts. Materials here are no longer maintained and reflect the state of the NCBI data and web site on the last course date, which was in the spring of 2008 for most courses. Nevertheless, many of these materials are still useful. Those from the technical workshops, the course for librarians and the mini-courses can serve as self-guided interactive tutorials, and all can serve as starting points for developing new teaching materials.
Courses and workshops
The current NCBI educational outreach program consists of NCBI-taught Discovery Workshops, Webinar broadcasts and a conference presence including tutorial sessions and live help at the NCBI exhibit booth.
Discovery Workshops will be offered beginning in the fall of 2010. The 2-day program consists of a set of four, 2.5-h hands-on sections emphasizing different aspects of the NCBI site. Each module uses specific examples to highlight important features of a set of related resources and tools and shows how to accomplish common tasks using these. The four modules focus on the following areas: Sequences, Genomes and Maps; Proteins, Domains and Structures; Using NCBI BLAST; and Human Variation and Disease Genes. These training courses are offered three times a year at the National Library of Medicine on the main campus of the National Institutes of Health in Bethesda, MD and four times a year in other areas of the United States. The off-campus courses are distributed across the eight regions of the National Network of Libraries of Medicine (http://nnlm.gov
) so that each region hosts a course every 2 years. The Discovery Workshops page has more information and a list of upcoming programs.
In addition to the in-person training courses, NCBI offers short web broadcasts, or Webinars, that are presented using the Adobe Connect web meeting software. Using this delivery mechanism, the only software needed to participate is a web browser. The sessions provide hands-on practice using the NCBI web site guided by an NCBI instructor. Webinars are presented to universities, medical schools and government research facilities in the United States. Multiple classrooms at multiple sites can participate in each Webinar. Current Webinar titles include: NCBI Overview; What’s New at NCBI; An Update on NCBI BLAST; and Genomes Update. A separate Webinars page has more details, upcoming broadcasts, links to materials and requirements for hosting a course.
The final component of the NCBI educational outreach program is the NCBI exhibit presence and associated tutorials at scientific conferences. NCBI has a traveling exhibit booth that is part of the marketing exhibit program at four major scientific meetings a year. NCBI Fact Sheets described above in the Documentation section of this review are available at the booth as well as current articles describing the NCBI services. More importantly, two NCBI Public Services staff members are available at the exhibit booth to provide live help on the NCBI site. Staff members provide a range of services: answering simple questions, troubleshooting problems with searches, and helping with designing search and data gathering strategies. At least twice per year, NCBI staff provides tutorial lectures as part of the exhibit program on a specific subset of NCBI tools such as Human Genome Resources or BLAST. The Conferences page presents the NCBI exhibit schedule and has more details. In addition, all NCBI training events and exhibits are announced through the NCBI news outlets and social networking sites presented in the next two sections.