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A Field Guide to GenBank® and
NCBI Resources:
NCBI’s Scientific
Outreach and Training Program
Biological sequence and structure information are now used in nearly every field of biological research. A working knowledge of these resources and standard computational biology tools are an essential part of every biologist’s toolkit. However, keeping up with these databases and tools can be challenging in this period of rapidly changing bioinformatics resources.
In order to help researchers keep abreast of enhancements and the increasing diversity of NCBI molecular biology resources, the NCBI service desk provides a free training program for biologists on the effective use of NCBI databases and tools. The course, called “A Field Guide to GenBank and NCBI Resources”, is designed especially for biologists who work at the bench or in the field but use sequence and structure data in their research. All researchers, educators and students who work with biological sequence and structure data should find this to be a useful introduction and survey of the available NCBI tools and databases. Because of the rapid expansion of the resources, even experienced NCBI users will likely learn something new and useful. Five members of the NCBI service desk comprise the Field Guide training staff: Peter Cooper, Susan Dombrowski, Wayne Matten, Rana Morris, and Eric Sayers. All are PhD- level biologists with a broad range of research and teaching experience that make them especially knowledgeable in the diverse interests and needs of the NCBI user community.
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Figure 1: Field
Guide Map shows the number of Field Guides held in each state through
April 2003.
The course consists of two main components: a three-hour lecture providing
detailed background on NCBI databases and a two-hour hands-on practicum
featuring biologically interesting examples that highlight key features
of the NCBI resources.
The Field Guide content is flexible and changes often to reflect shifts in emphasis
and content of the NCBI Web resources. The focus of the Field Guide can also
be tailored to the specific interests of the audience. Special Field Guides have
been presented that emphasize resources for marine organisms, insects, and agricultural
plants. Components of the Field Guide have also been offered as parts of specialized
short courses and workshops, notably the Cold Spring Harbor Laboratory’s “Computational
Genomics” course, the Jackson Laboratory’s “Experimental Genetics
of the Laboratory Mouse in Cancer Research”, the “MR4 Malaria Bioinformatics
Workshop” at the ATCC, and “the Biology of Parasitism” summer
course at Wood’s Hole Oceanographic Institution.
In addition to the Field Guide, the training staff also offers more detailed
modular courses that focus on a particular subset of the NCBI resources. A BLAST
module is available that provides more extensive hands-on training using the
Web BLAST services and practical experience setting up and using standalone BLAST.
A separate module providing more in-depth training in the use of NCBI structure
databases and tools will premiere this summer at the University of Pennsylvania.
Modules will soon be available that focus separately on Entrez and genomic resources.
The Field Guide continues to grow in popularity. Since the initial offering at
Yale University in November of 1998, the course has been presented 140 times
in 37 States and Puerto Rico to approximately 8,000 participants. The map on
the newsletter front page shows the geographical distribution of Field Guide
host institutions to date. At the time of this writing, there are 35 courses
scheduled for the remainder of 2003. The course is updated each time it is given
and provides the most current view of the NCBI resources available anywhere.
For this reason, many institutions offer the Field Guide on a regular schedule,
including Vanderbilt University, the University of Michigan, the University of
Virginia, the Mayo Clinic, and the University of Pennsylvania. A schedule of
upcoming and past Field Guides is available from the FieldGuide Home Page referenced
below. Anyone who would like to attend one of the courses listed there should
contact the host institution through the links provided.
NCBI provides this training free of charge at educational institutions and government
laboratories and pays all travel expenses for two NCBI instructors to conduct
the course. To host a course, an institution must have the appropriate facilities:
a lecture hall and a teaching computer classroom. The host institution must also
be able
to attract a minimum audience of 50 people and must manage course registration.
The audience size requirement is rarely a barrier; at larger university settings,
audience size often exceeds 200 people. When practical, we also ask that the
host institution open registration to include people outside their institute
in the training. In many cases, participants have traveled hundreds of miles
to attend Field Guide courses at host institutions.
For more information about course content and links to the most recent lecture
materials and hands-on exercises, see The Field Guide Home Page at:
| www.ncbi.nlm.nih.gov/Class/FieldGuide |
Additional details about hosting the NCBI courses are linked to the Field Guide
Home Page. Courses are now being scheduled for late fall of 2003 and early
2004.
Anyone interested in scheduling a course should contact Peter Cooper at: cooper@ncbi.nlm.nih.gov
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