Internet Resource Guide

A Compilation of Essential Websites for

Penn State B.S. Biology Majors



Provided By: Larry Klomps



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Table of Contents
Information About This Guide...............................................................3

Intended Audience & Purpose................................................................3

Content and Material ..............................................................................3

Assumptions about the Reader ...............................................................4

Guide Organization.................................................................................4

Hints and Tips.........................................................................................5

Resources Found in this Guide................................................................5
General Internet Sites...............................................................................6

RCSB Protein Data Bank...............................................................6
PROSITE Protein Database...........................................................7
BioOne.......................................................................................... 8
Biology News Net..........................................................................9
Publications..........................................................................................10
Journal of Cell Biology.................................................................10
Thomson Reuters Web of Knowledge
SM
.......................................11
The Statistical Abstract of the United States.................................12
Catalog of U.S. Government Publications....................................13

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Information About this Guide
This section provides information about what one can expect to find relevant to
one's field of study, research, or work in this guide. Thus, it will introduce who
should read this guide, its content and organization, and prior knowledge needed to
use this guide effectively.

Intended Audience & Purpose
The purpose of this resource guide is to provide a collection of practical internet
resources for undergraduate students majoring in biology at Penn State. Students
who are in 5th semester standing or higher may find this guide more useful than a
freshman biology student due to advanced subject matter. However, underclassman
can still benefit from the content provided in this document, such as sites for
researching various topics. That being said, this guide will offer valuable reference
materials to enhance productivity for students at different points in their studies.

Content and Material
This guide includes multiple links to web sites that a biology student would find
important to his or her everyday studies. Some subject matter in these sites include
biochemistry and molecular biology, cell biology, proteomics, microbiology, and
ecology. Also incorporated into this guide are links to journals for students
conducting research that are in need of primary literature. Likewise, one can
exploit the aforementioned resources or see what cutting-edge research is taking
place with additional links to scientific news and discussion boards.




About this Guide

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Assumptions about the Reader
It is recommended that readers of this guide are biology majors or were previously
enrolled in related coursework. Some suggested PSU courses that are necessary in
understanding the material presented in this guide are BMB 401, CHEM 212,
BIOL 110, 230, and 240. If one has not yet completed these classes or is currently
enrolled in one, there is still plenty of useful resources in this guide to aid the
developing biologist. If one cannot understand a topic, look it up, biology is an
investigative science!

Guide Organization
The most efficient way to use this guide is to refer to the headings listed in the
Table of Contents. The resources in this guide are divided into two broad
categories: General Internet Sites and Publications. Provided under these two
sections are four web sites with brief abstracts that offer pointers about each site
and highlights unique attributes of those sites.
Finding good publications can be a real pain. Thus, a guide that offers sites to
reduce the headaches associated with finding good publications is essential to any
student doing research. Sites intended for upperclassmen use are listed first, with
subsequent sites accommodating students at different levels of biological
coursework.







About this Guide

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Hints and Tips
Being a Penn State student comes with a multitude of resources available
both on and off campus, especially for biology students. To ensure student
awareness of these resources, this guide will use three distinctive pictures for
sites specific to Penn State students.

o This caption will appear by sites that contain databases of
publications. Students involved with research are encouraged to take
advantage of the wealth of primary literature available to them for
citing sources applicable to their own.

o There are a lot of interesting things going on in the scientific
community. This caption will appear next to sites that contain
interesting topics in the news to highlight what biology students can
do in the lab at Penn State or in a job post-graduation!

o The library at Penn State has proved to be invaluable for accessing
sites that students would usually have to purchase site access. This
caption will indicate sites that should be accessed through
libraries.psu.edu, located under the databases tab, unless one would
like to pay for their own access!
Resources Found in this Guide
In the sections below, one will find resources pertinent to the biological studies.
Within each main category, sites for upperclassmen use are listed first, with
subsequent sites suited for students of different semester standings. Remember to
pay attention to graphics for recommended site usage.

About this Guide

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General Internet Sites
RCSB Protein Data Bank
http://www.rcsb.org/pdb/home/home.do
Abstract: Students researching macromolecular structure of proteins will benefit
greatly from this site. The Protein Data Bank (PBD) is a comprehensive archive of
biological macromolecules such as DNAs, RNAs, and proteins. This resource is
also essential to biochemists as it allows for viewing secondary, tertiary, and
quaternary structures of proteins and keys motifs within a specific protein.
Searching within this site is made easy by the "Explore Archive" option that allows
browsing by polymer type, taxonomy, and enzyme classification, to mention a few.
Tips for using this site:
To download structures click on the "Download Files" link under the section
titled "Tools." Enter the PDB IDs and separate them by commas to retrieve
the desired structures.
To obtain multiple file formats of the molecule, such as NMR restraints,
mark the check boxes in the preceding pointer and click "Next." Save the
files to a flash drive or to the desktop.
One can also compare structures of molecules under the "Tools" section.
Once one follows that link, fill in the two provided boxes with the two
polypeptides in question, select the comparison method, and click compare.
Job listings by PBD can also be found by clicking on "Careers" under the
"Home" box on the left. This is a great resource for a student looking for a
career; PBD is currently looking for potential employees with a B.S. in
biology or biochemistry!



General Internet Sites

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PROSITE Protein Database
http://prosite.expasy.org/
Abstract: This site provides a very useful tool for students running protein assays.
It consists of a search box for the input of protein names and allows for quick
viewing of consensus sequences and contains documentation entries for domains,
homologs, and functional sites. Additionally, one can scan sequences against
PROSITE patterns and profiles with the option of an advanced scan. This site is
great for viewing peptide sequences for quick identification of important residue
R-groups.
Tips for using this site:
In the search box, on the left hand side, type the name of a protein of interest
to retrieve a description of its action in the cell, including its peptide
sequence.
One can also browse the data bank of proteins by clicking on one of the four
links under the "Browse" section located in the middle of the page.
To compare one's sequence, enter the peptide sequence in the box located at
the bottom left corner and click "Scan."






General Internet Sites

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BioOne
http://www.bioone.org
Abstract: This website contains a wealth of bioscience research journals for many
fields of biology including, but not limited to, teaching, embryology, zoology, and
cell biology. Journals are listed alphabetically by title, publisher, or collection that
allows for a broad search. When visiting this site, expect an easy-to-use search tool
that helps narrow results for quick journal evaluations. Journal articles are
downloadable as PDF files or can be viewed directly on the webpage. Overall, this
site has excellent content organization, provides user-friendly browsing tools, and
offers a multitude of research journals for any biological discipline.
Tips for using this site:
This sites simplicity compliments its effective search tool. To search for a
journal article click on "Advanced Search" in the upper right hand corner of
the screen. An expanded search box will then appear on the left.

One can also save a search and view it later by inputting a name and
description in the box beneath the search tool.

There are several browsing modes as well. One can browse by title,
publisher, or collection by selecting and option from the "Browse" link.







General Internet Sites

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Biology News Net

www.biologynews.net
Abstract: Any biologist looking to follow current and interesting news in biology
can rely on this site to deliver it. This site concisely presents news in biological
research and further captures the reader's interest with visually stimulating
graphics. In addition, the news articles offer easy readability for any person that
might not specialize in biology but is interested in the topic. The site also provides
links to many other scientific sites and discussion rooms for further topical
investigation. Overall, this site keeps a biologist up-to-date with current research in
biology, such as epigenetic regulation of oncogenes, which is great for research
brainstorming.
Tips for using this site:
To view articles click on the "Full article" link located at the bottom of the
article summary. To get back to the home page where other articles are
listed, click on the large Biology News Net banner on the left.

A fun item to mention on this site is the view counter located on the lower
left of each article box to show how many other people have accessed that
article. It offers a good way to gauge how interesting that article might be!





General Internet Sites

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Publications
Journal of Cell Biology

http://jcb.rupress.org/
Abstract: The Journal of Cell Biology is a great resource, especially for
upperclassmen, on research in intracellular signaling, such as directed chromatin
signaling, proteomics, and genomics. This site puts the latest articles at one's
fingertips and offers a section titled "Research Highlights" in which it gives a brief
synopsis of the study and a link for further reading. In addition, there are many
links to news, multimedia, and an archive of previous publications. This site has
been previously recommended by a professor of biology, a good indicator to its
importance and significance.
Tips for using this site:
On the left hand side of the site the current issue is displayed. Click on the
"View Table of Contents" link. All the articles in that month's issue will be
present with abstracts. To see the abstracts, all one needs to do is hover the
cursor over the article title.
The site also contains alerts and feeds to help one stay current with research
published in this journal. Click on "alerts & feeds" to subscribe to a feed
such as Facebook or Twitter.
One can also access the Journal of Experimental Medicine or the Journal of
General Physiology, hyperlinked in tabs on the upper right of the site. There
will be some overlap of content, but they are two other great sources for
primary literature and leading research.



Publications

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Thomson Reuters Web of Knowledge
SM
apps.webofknowledge.com
Web Of Knowledge
SM
is an online index for fast searching of journals and
databases. It includes three search parameters that help fine-tune document
searching.

Abstract: Web Of Knowledge
SM
contains a great database called Biological
Abstracts that serves as a search engine for published research. This site should
be of particular interest to cell biologists and biochemists since these categories
contain the greatest amount of publications. For instance, if one searches for BRaf,
the site lists publications that discuss the oncogene and its prevalence in
melanocytic nevi. Nonetheless, this site empowers one with efficient browsing and
for less time on the web and more time in the lab.
Tips for using this site:
Most importantly, access this site via libraries.psu.edu and click on
databases. Select "B" to list databases starting with that letter and
click on "Biological Abstracts." This will give one full access to the
site.
A unique feature of this site is its guided search. It allows the user to
choose a broad category of interest and refine search results with
subcategories. First, enter the search word or phrase and wait for the
results to load. Second, on the left hand side of the page is a blue box
for search refinement, select boxes in the "Subject Areas" section and
click "Refine."
If one wishes to save their search, click on the link "Search History"
and select the searches you wish to save. Save the searches to a flash
drive for later access.




Publications

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The Statistical Abstract of the United States
http://www.census.gov/compendia/statab/
Abstract: This site offers a summary of statistics on the social, political, and
economic organization of the United States. The site provides a wealth of data for
students interested in a statistical representation of occupational employment in
one's field. The site categorizes this data under sections on the left hand side of the
page. The information included also serves as a guide to other statistical
publications available to the public. Follow the example below to find life sciences
(biology falls in this category) and healthcare related job growth.

Example:
http://www.census.gov/compendia/statab/2011/tables/11s0813.pdf
Click on the above link to find statistics on employment, earnings, and growth in
science. This will load a PDF document representing a table from the Bureau of
Labor Statistics' Occupational Employment Survey. Of particular interest is the job
growth for the life scientist. According to the table, there was a mean annual
growth of 3.7% for Life Scientists. One can use this table to compare job growths
and use it to evaluate future job opportunities.
Tips for using this site:
On the left hand side of the page scroll down and click on "Science and
Technology." Another box will pop up, click on "Employment." This will
take one to statistical data for employment in the sciences.
On the right hand side of the page are useful links for further investigations.
Population ecologists might find it useful to click on the "Births and Deaths"
link as it provides interesting statistics about the U.S. growth rate. One could
use it to postulate when the U.S. reach its carrying capacity.




Publications

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Catalog of U.S. Government Publications
http://catalog.gpo.gov/
Abstract: The Catalog of U.S. Government Publications (GCP) is a search tool for
finding publications from the U.S. government agencies. Users can enter words or
phrases under the advanced search option, which often yields more than enough
results. For instance, users can type in different viral strains of the flu or smallpox
and find hundreds of articles on its use in bioterrorism or its epidemiology .
Moreover students studying ecology could use it to look up literature on a specific
species of bird. Overall, the site is easy to navigate with tabs located at the top to
search different pages quickly. Ecology students, see the below example for a
document on Mountain Plovers, a threatened species of bird.
Example:
Title: Mountain Plover (Charadrius montanus)
Publisher: Wildlife Habitat Management Institute
Author: Holly L. May
Reviewed by: Fritz Knopf

This document outlines habitat requirements of the mountain plover and how
landowners can develop a species-specific management plan. Moreover, the
document lists behaviors, such as polyandry, ranges, and habitat requirements for
mountain plovers, which is critical in the preservation of this threatened species.
This article is a great example of a document that can be cited in one's own
introduction in a research paper. Furthermore, the document was reviewed by Fritz
Knopf, a well-known ornithologist and has done much of his own research on this
species.
Tip for using this site:
This site is really basic, just click on the "Advanced" tab to bring up a quick
search for a topic of interest!
Multiple search parameters will show up under this tab, one should keep the
search simple and sort the results by date to show the most recent updates.
One can also select multiple documents for viewing by selecting the
respective check boxes and clicking "View Selected."
Publications