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Department of Biological Sciences,
Hunter College of CUNY
UNDERGRADUATE RESEARCH TECHNIQUES FACILITY |
Module XV.
WWW Bioscience Research Resources: Some Examples
This is a sampling of WWW offerings of value to researchers
in the biosciences.
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INSTRUCTIONS: This module is completed On-Line.
Read introductory material, then examine each
linked Website briefly, in sequence. Return via
Back arrow. |
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These sites were active as of 1/03; subsequent
changes in content or address are possible. If any such
problem arises, proceed to next site. |
Summary of Module Contents:
- Model Organisms:
Websites focusing on particular organisms that are of
enormous value to basic biomedical research.
- Electronic Journals: A
few of the peer-reviewed biosciences journals now on the
WWW.
- Research Literature: Accessing
and using the National Library of Medicine research
literature database ("PubMed").
- Institutions: A
sampling of teaching and research institutions relevant
to the biosciences.
- Corporate WWW Sites: A
few of the many companies, now online, that provide
biomedical research supplies and equipment.
- Other Research Resources: A
selection of WWW sites useful to biomedical researchers
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Use the {--> next}
link to bring each next step to top of scroll window. |
A significant number of WWW sites now
specialize in information on "Model" organisms used
extensively In biomedical research. Such organisms have certain
characteristics that are particularly valuable to researchers,
making it much easier to do experiments and/or to analyze the
data obtained. Typically, "Model" organisms are
utilized for BASIC research, that is, research that attempts to
obtain such fundamental information about living things that it
can help to understand mechanisms at work in ALL organisms,
including humans.
The best-known "Model" organism is
probably the fruit-fly, Drosophila melanogaster. It has
been invaluable in genetics, developmental biology, and many
other fields, principally because of characteristics such as very
short life cycle, small size and ease of culture, and readily
visible genetic traits. Information about Drosophila, as
well as other equally valuable organisms, is accessible on-line
at the WWW Sites listed in exercise 1. {-->
next}
EXERCISE #1. MODEL ORGANISMS.
Pay a visit to any three of the following
sites (click on active links).:
a. The
bacterium Escherichia coli ..........{--> next}
b. The yeast Saccharomyces
cerevisiae ..........{--> next}
c. The nematode worm Caenorhabditis
elegans ..........{--> next}
d. The
fruit-fly Drosophila melanogaster ..........{--> next}
e. The zebrafish Danio
(Brachydanio) rerio .....................{--> next}
f. The frog Xenopus laevis
.....................{--> next}
g. The "wall
cress" Arabidopsis thaliana
(a weed - the "fruit-fly" of plant research).
..........{--> next}
One of the problems with material appearing on
the WWW is that anyone can present almost anything. This means
that it may be difficult to determine the reliability of
information obtained from WWW sites. For scientists, it is
particularly important that there be evidence of expertise before
accepting ANY WWW information as valid.
With this in mind, please note that the
journals listed below are "peer-reviewed". When
research papers are submitted to such journals, their contents
are scrutizined in detail independently by reviewers (usually at
least two) who are professional scientists with expertise in the
relevant field, and whose identity is unknown to the author(s) of
the paper.
No paper is accepted for publication in a
peer-reviewed journal unless it meets reviewer criticisms
(frequently after revision) and receives approval of the
journal's Editorial Board. Many papers are, in fact, rejected by
peer-reviewed journals. This does not mean that all information
appearing in such journals is absolutely correct. Rather, it
means that the quality and reliability of their information can
be expected to be high because it is maintained by professional
screening standards.
While many of the biosciences journals
currently on the WWW are classical print-media ones that make
available on-line Abstracts and search functions, some provide
electronic versions of entire printed papers on-line. There are
also a number of WWW journals in the biomedical sciences that are
totally electronic; that is, they appear ONLY on the WWW, and are
not issued in printed form. Some examples in each of these
categories are provided in the next exercise. {--> next}
EXERCISE #2. Examples of peer-reviewed
journals relevant to the biomedical sciences, now represented on
the WWW {--> next}
Electronic versions of printed journals,
examples:
a. The Journal of
Biological Chemistry (entire articles available){-->
next}
b. Science
(abstracts available){--> next}
c. Nature
(abstracts available) {--> next}
Totally electronic journals, an example:
a. Emerging
Infectious Diseases (entire articles available) {--> next}
Accessing the National Library of Medicine
literature database ("PubMed").
A most useful URL is that of the PubMed
literature database, which will enable you to search for papers
by topic in most of the biosciences journals. The next exercise
will introduce you to this on-line service. PubMed does not
provide the whole document or journal, but it will give you
abstracts and, in some cases, links to free online copies of the
papers. By going through abstracts on-line, you can conduct a
rapid, efficient search prior to visiting the library for printed
copies, or accessing the library's electronic journal
subscriptions to obtain the full papers.
{--> next}
EXERCISE
#3: Using PubMed (a resource of the U. S. National
Library of Medicine)
- Click the following PubMed
URL: http://www.ncbi.nih.gov/entrez/query.fcgi
- Look
at the site; note typing box near top of page
- Read
search instructions just below the box.
- Start
by typing in "hemoglobin" as a topic for which
we seek literature, and hit "Go".
- How
many documents are retrieved?
The total is given in the grey area above the first
reference, together with the no. of refs. displayed at a
time, plus the number of pages of refs. found.
- Since
"hemoglobin" is a broad research topic, PubMed
gives you far too many citations to be useful
(>80,000!). Narrow your search by entering a second
key word - "oxygen" - together with
"hemoglobin", and hit "Go" again..
- Is the
number of documents retrieved now significantly lower?
You will need to narrow it further by entering more key
words.
- Try
adding a term that is still more specific: "carbon
monoxide". Next, add "binding site". Do
you now recover a reasonable number of documents of
interest?
- Examine
ONE of them briefly by clicking on it. Note that the
abstract appears, plus an options bar. Return to the
previous page via the BACK button.
- Terms
other than article keywords can be entered, such as
author's name, journal title, and dates. These can
facilitate searches considerably. test this by adding
"Smith" as a final term above - how many refs.
are retrieved now?
- Return
to the RTF Website via the BACK Button or RTF URL.
Perhaps you have heard about a scientist,
research project, or training program based at a particular
academic or research institution, and would like to know more.
Most research and educational institutions now have WWW Sites
offering comprehensive information about academic and research
programs, course offerings, and even campus activities. A
sampling in the biosciences is provided in the next exercise. {--> next}
EXERCISE #4. Academic and Research
Institutions: Some Examples in the Biosciences
Pay a brief visit to each of the following
Sites:
a. Dept.
Biological Sciences, Hunter College (New York) ..........{-->
next}
b. The Marine Biological Laboratory (Woods Hole,
MA)..........{--> next}
c. The European Molecular Biology
Laboratory (Heidelberg).......... {--> next}
d. The National Science Foundation (Wash., DC)..........{--> next}
e. The National Center for
Infectious Diseases (Atlanta, GA)..........{--> next}
Additional valuable information can be obtained
from corporate WWW sites. There are now a great many biomedical
supply and research instrument companies on the WWW. We present
here four for your examination. The first, Beckman Instruments,
is a manufacturer of many types of equipment, including
centrifuges. The second, Molecular Dynamics, makes specialized
microscopes such as confocal fluorescence microscopes, and other
types of analytic equipment. The third, Sigma Chemical Co., sells
biochemicals and the fourth, Fisher Scientific, is a general
supplier of laboratory items for biomedical research. The printed
catalogs of the last two are on our Tech Facility shelf, and
their WWW sites contain both catalog information and the capacity
for on-line ordering.
EXERCISE #5. Make a brief visit to each
of the following (click on the links provided here):
Beckman Instruments
Amersham Biosciences
Sigma-Aldrich
Fisher Scientific Co...........{-->
next}
There are many other on-line WWW resources
utilized by biosciences researchers. These include both databases
and research tools. Some examples follow:
(a) A database: It is possible to access and
search all publicly available DNA base sequences using
"GenBank". It is also possible for researchers to
SUBMIT such sequences electronically (using an on-line form) for
inclusion in GenBank.
(b) A research tool: The National Institutes
of Health (NIH) provides a digital image enhancement and analysis
program (software) at no cost, called "NIH Image".
(c) Information about another research tool:
the NIH Molecular Modeling WWW Site.
Links to these examples are provided in the
next exercise. {--> next}
EXERCISE #6. Pay a brief visit to each of
these on-line Research Resources: {-->
next}
a. GenBank ..........{--> next}
b. NIH Image {-->
next}
c. NIH Molecular Modeling {--> next}
THIS COMPLETES MODULE XVI
