The Help Desk

Help Desk assistance is available from 8:30 a.m. to 5:30 p.m. Eastern Time, Monday through Friday. Two email addresses are available, info@ncbi.nlm.nih.gov and blast-help@ncbi.nlm.nih.gov. The vog.hin.mln.ibcn@ofni address is for any type of inquiry, including questions about services; how to get started using the NCBI tools for a particular research problem; reports of technical problems; press inquiries; and comments or suggestions about NCBI resources. The vog.hin.mln.ibcn@pleh-tsalb address is for questions and comments regarding sequence similarity searches using BLAST tools and databases. The Help Desk phone number is 301-496-2475.

email questions are answered as expeditiously as possible, usually within a day of receipt of the question. However, those that require extended investigation may take longer. Questions are usually handled directly by members of the User Services staff, although some are referred to a specific database development team for attention.

Examples of question topics include: data submission protocols, including the use of BankIt and Sequin (Chapter 12); finding summary information about a gene or disease; using Entrez (Chapter 15) to find sequence records for genes and proteins; choosing the best BLAST service to use for a particular application (Chapter 16); how to interpret BLAST results; how to display and manipulate three-dimensional structures with Cn3D (Chapter 3); how to display genome data using the Map Viewer (Chapter 20); how to print or save search output; how to set up sequence databases and install NCBI software locally; and which databases to use for a specific research question. We also accept reports of possible data errors, suggestions of new features or content to include in databases, and reports of system bugs or Web problems. The NCBI also receives a number of press inquiries about the research applications of our services, bioinformatics in general, and various genome projects. Occasionally, a high-school student will submit questions for a classroom assignment, providing a special outreach opportunity to young scientists.

Because of the genetic focus of many of NCBI resources, we receive a number of questions from the general public regarding medical issues. The NCBI Help Desk staff can neither provide direct answers to medical questions nor give medical advice or guidance. However, we do provide suggestions on how to search our resources for information on the gene or condition of interest and refer users to the National Library of Medicine (NLM) customer service group for further assistance with PubMed (Chapter 2), MEDLINEplus, and ClinicalTrials.gov. We also refer them to outside organizations that can provide information on such topics as support groups and sources of medical advice.

Questions about PubMed are handled by a separate customer service group within the NLM. Their direct address is vog.hin.mln@vrestsuc, and their phone number is 1-888-FIND-NLM. PubMed questions that are received at the NCBI Help Desk are forwarded to NLM.

Tutorials on the Web

Web-based tutorials for BLAST, Entrez, Cn3D, and PubMed are currently available, with additional topics under development. Tutorials are produced on a collaborative basis by database development and User Services staff.

About NCBI

In keeping with the “plain language initiative” at NIH, the About NCBI section of the NCBI Web site presents many fundamentals of NCBI's bioinformatics tools and databases, including a science primer covering such topics as molecular genetics, genome mapping, Single Nucleotide Polymorphisms (SNPs) (Chapter 5), and microarray technology (Chapter 6). A model organism guide presents various model organisms and their uses in laboratory settings. As an introduction and orientation to NCBI's multifaceted Web site, the About NCBI section appeals to the general public, educators, and researchers alike.

NCBI Site Map

The NCBI Site Map serves as a guide to NCBI resources. It provides a comprehensive, linked list of resources, along with a brief description of each resource. An effective way to locate a resource of interest within the Site Map is to perform a Find in Page search, a function that is built into all commonly used Web browsers.

Publications

The NCBI News is a quarterly newsletter that includes articles on new services, new features, and basic research at NCBI, as well as how to use selected resources for common applications. The newsletter is available free of charge and is offered online and by print subscription.

The User Services group also prepares fact sheets, brochures, and other public information materials to describe and illustrate NCBI services. A list of available materials is provided in the About NCBI section of the Web site, under News.

Overview articles entitled GenBank and Database Resources of the NCBI have also been published recently in the annual database issues of Nucleic Acids Research (1-3).

Exhibits at Scientific Meetings

NCBI exhibits at approximately 15 scientific meetings per year, providing an opportunity for a wide range of researchers, students, and teachers to see demonstrations of NCBI resources and interact directly with NCBI staff. The current exhibit schedule is posted on the NCBI Web site in the About NCBI section, under NCBI at a Glance.

Workshops are offered at select scientific meetings and include the standing workshops described below in the Training section, but workshops also can be customized for particular audiences. Meeting organizers who would like to invite NCBI to offer a workshop are encouraged to do so.

Training Courses

NCBI has a growing training program consisting of full-day, half-day, and two-hour courses that are usually a combination of lecture and computer-based formats. There are also advanced courses that are given over a more extended time period. Each is described briefly below, and further information on the training programs can be found in the Education section of the Web site, under NCBI Courses.

The NCBI Learning Center

In addition to communication by email and phone provided through the Help Desk, a regular research consultation service provides one-on-one support for researchers in the NIH community. The consults are available by appointment and are provided in 1-hour time slots at the NIH Library as well as the NCBI training facility. Because of the success of the program, this type of service may be offered by appointment at selected scientific meetings in the future.

CoreBio

An innovative training program that began in 2001 aims to train molecular biologists for a new type of career as bioinformatics specialists who provide institutional support for users of computational biology tools. The NCBI Core Bioinformatics Facility (referred to as the CoreBio program) currently functions to train and support a network of bioinformatics specialists serving individual Institutes at NIH. NCBI's CoreBio facility trains Core members identified by their respective institutes in the use of its bioinformatics tools. The Core members, in turn, support the use of NCBI tools and databases by researchers at their institutes.

The training is provided over a 9-week period, with students attending lectures and completing practical exercises in the morning and returning to their regular workplace in the afternoon. The coursework centers on one major topic each week and follows the rough schedule given below:

WEEK 1: Introduction to the Sequence Databases

WEEK 2: BLAST

WEEK 3: The Human Genome

WEEK 4: Genomic Biology

WEEK 5: Molecular Modeling

WEEK 6: Web Page Development

WEEK 7: Setting Up a BLAST Web Server

WEEK 8: Interaction with Users

WEEK 9: Practicum

During week 9, the students pursue an institute-related project with the assistance of NCBI instructors. These projects run the gamut from the compilation of specialized datasets and data mining to the creation of novel BLAST interfaces and the construction of new data display tools. Students also develop a Web page to support the services they are developing for the respective Institutes at the NIH.

Although currently a NIH-based program, other organizations are welcome to consider using the program as a model for development of similar initiatives to meet their bioinformatics support needs.