Department of Biological Sciences,
Hunter College of CUNY


Module XV.

WWW Bioscience Research Resources: Some Examples

This is a sampling of WWW offerings of value to researchers in the biosciences.

INSTRUCTIONS: This module is completed On-Line.   Read introductory material, then examine each linked Website briefly, in sequence.  Return via Back arrow.
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:

  1. Model Organisms:   Websites focusing on particular organisms that are of enormous value to basic biomedical research.
  2. Electronic Journals:  A few of the peer-reviewed biosciences journals now on the WWW.
  3. Research Literature:  Accessing and using the National Library of Medicine research literature database ("PubMed").
  4. Institutions:  A sampling of teaching and research institutions relevant to the biosciences.
  5. Corporate WWW Sites:  A few of the many companies, now online, that provide biomedical research supplies and equipment.
  6. Other Research Resources:  A selection of WWW sites useful to biomedical researchers

Use the {--> next} link to bring each next step to top of scroll window.

1.  Model Organisms

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}


Pay a visit to any three of the following sites (click on active links).:

a. The bacterium Escherichia coli ..........{--> next}
The yeast Saccharomyces cerevisiae   ..........{--> next}
The nematode worm Caenorhabditis elegans   ..........{--> next}
The fruit-fly Drosophila melanogaster ..........{--> next}
The zebrafish Danio (Brachydanio) rerio .....................{--> next}
The frog Xenopus laevis .....................{--> next}
The "wall cress" Arabidopsis thaliana
     (a weed - the "fruit-fly" of plant research). ..........{--> next}

2.  WWW Electronic Journals in the Biosciences

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:
The Journal of Biological Chemistry (entire articles available){--> next}
Science (abstracts available){--> next}
Nature (abstracts available) {--> next}

Totally electronic journals, an example:
Emerging Infectious Diseases (entire articles available) {--> next}

3.  Research Literature:

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.

Read all steps before proceeding, as they will not be visible while in the PubMed site! Return via "Back" button as necessary.
Alternatively, go to a copy of EXERCISE #3 ONLY; print it out using "Print", then return via "Back" button (click here: COPY)

  {--> next}

EXERCISE #3:  Using PubMed  (a resource of the U. S. National Library of Medicine)

  1. Click the following PubMed URL:
  2. Look at the site; note typing box near top of page
  3. Read search instructions just below the box.
  4. Start by typing in "hemoglobin" as a topic for which we seek literature, and hit "Go".
  5. 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.

  6. 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..
  7. Is the number of documents retrieved now significantly lower? You will need to narrow it further by entering more key words.
  8. 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?
  9. 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.
  10. 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?
  11. Return to the RTF Website via the BACK Button or RTF URL.

4.  Institutions

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}
The Marine Biological Laboratory (Woods Hole, MA)..........{--> next}
The European Molecular Biology Laboratory (Heidelberg).......... {--> next}
The National Science Foundation (Wash., DC)..........{--> next}
The National Center for Infectious Diseases (Atlanta, GA)..........{--> next}

5.  Corporate WWW Sites Useful In Biomedical Research

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


Fisher Scientific Co...........{--> next}

6.  Other Research Resources in the Biosciences

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}
GenBank ..........{--> next}
NIH Image {--> next}
NIH Molecular Modeling {--> next}