|
|
Exercise 1: Introduction to
Bioinformatics
Internet as a Research Resource & Search
Strategy Basics
Note 1: You should get in the habit of bringing a
disk to class to save your log and any other useful files.
You may use either a floppy or zip disk.
Note 2: This exercise is in the format and design
of later exercises, but it is not graded for points since
the basic material should be review. If you turn in answers
to the summary questions, you will receive feedback.
Objectives:
1. Gain a basic appreciation of what bioinformatics is
and how it can be used.
2. Become familiar with on-line resources helpful in
learning bioinformatics.
- Be able to comfortably navigate on the Web.
- Become familiar with the class web site.
- Be able to use search engines efficiently.
- Identify and use support sites relating to
bioinformatics.
- Be able to evaluate source and quality of information
obtained.
3. Learn to use a log as an organizational resource and
tool.
- Keep track of bookmarked sites.
- Annotate sites and resources; collect information;
note location of downloaded files.
- Use as resource for homework assignments and papers,
including but not limited to content and references.
Introduction:
Although these exercises are being introduced in a PC
computer lab, the exercises are not platform
specific. You may choose to use either Netscape or Explorer
as the browser. Please note; however, that you'll want to
use Netscape when using plug-ins for viewing molecular
models. This introduction is geared [or tries to be]
both to those with little experience using the Internet and
web browsers, and to those with a significant amount of
experience.
If instructions seem to move along too fast, ask for help
from other students and from me. If instructions seem too
detailed, and you just want to get on with it, please
do.
If using the IMac labs, you will need a 100 or 250 MB zip
disk to save your work. Floppy drives have been fazed out in
favor of zip drives. You also may print your work to the
printer in the lab you are working. You need to supply your
own paper. For the mobile lab, we do not yet have a priner
available.
It is strongly suggested that you keep a log of
your sessions on-line. Although you may bookmark sites while
using a lab computer, the bookmarks are removed daily. Even
if you are using your own computer, try using a log anyway.
You can add comments, store specific database sources, and
copy/paste whole pages of information for future use. A
current version of Word is quite useful for a log, because
URLs [Web addresses] can be turned into active link
sites. In other words, you can carry your bookmarks with
you, without having to retype them. [For more on logs,
go to Keeping
a log.]
There are summary questions at the end of this
section. Read them through before you start browsing. You
can answer them as you go, or answer them after browsing the
following sites. Points = 0. Due 9/4.
[top of
page]
Pre-Exercise:
1. Spend some time becoming familiar with what is
available on the class web site, if you haven't
already done so. Feel free to print out sections to use as
reference. In the past, many have found that having a hard
copy of the exercises for reference was a useful addition to
using the online version.
2. Optional. If you are not familiar with
what the World Wide Web and the Internet are, or you would
like to become a little more familiar, go to
http://www.december.com/web/text/
This online course covers a broad range of topics of
interest to beginning users of the Web.
[top of
page]
Exercise:
Start a log by opening a Word document. You can size this
window to be easily toggled when the browser is open, which
you have also sized and positioned so that you can see both
windows. Alternatively, you may prefer to work with both
windows maximized and toggle between them by using the
navigation bar.
When using you own computer or one to which you have
regular access, I strongly recommend that you bookmark the
sites you like. [Bookmarks are regularly removed from
school computers, but they are still handy during a single
session, so give them a try.]
1. Log on and open a browser. In this first
section, there are links to representative resource
sites providing useful background support for
bioinformatics. Also included is a site introducing an idea
for future development in the virtual world of information
access. Briefly explore each one, noting what they have to
offer locally and what links to other sites may be
available.
[top of
page]
2. Before you get too far along in your log, it is
good to know what you should be doing to record the
necessary information for the sites you visit. This is
useful for several reasons: 1) you want to return to a site
or find a specific image or piece of information again; 2)
you want to share your discovered site with someone else; 3)
you need to cite your references in a report, paper,
or on a web page. Just as you need to cite print references,
web sites need to be cited as well. The related issue of
plagiarism is also important. You will need to
clearly distinguish your own original work and writing from
that of others. Briefly explore the following sites. You can
refer back to them as needed.
3. So far you have been visiting sites of static
pages. These are being served up from both local and remote
servers. It's nice having all these convenient links to
click on. But what do you do if you want to find out about
something not linked right in front of you, or you want to
see what else might be available? You need to do a
search. [For those of you rolling your eyes and
yawning, feel free to skip ahead. However, just be careful
that you don't miss something important.] Being able to
conduct efficient and productive searches is a skill crucial
to using the Internet and the databases associated with it.
You will be learning how to search in a variety of contexts
throughout the semester. For those of you not used to
general searching on the web, you should try the following
as a way of becoming familiar and comfortable in digging up
information and resources of interest.
Look at some general browser search engines, such as
Google Dogpile, Ask Jeeves, Yahoo, and [among
many others]. When looking for something
specific, sometimes you don't quite know where to start; or
you thought you did, but came up empty. Sometimes, you just
want to find out what is available in a general category.
The search engines can be very useful, if you know how to
use them efficiently. Different search engines will give
different results.
- Try out a broad term, such as "bioinformatics" or
"genomics", on three different browser search engines.
You can pick them from a list, by clicking on "Search" on
your browser navigation bar or type in their URLs. I
personally like
[www.google.com; www.yahoo.com; www.ask.com]
because they happen to work well in the science
fields, whereas some of the others tend to have more
depth in other areas.
[www.dogpile.com] can search other search engines
as a group, therefore can be extremely useful when
hunting for hard-to-find items. See what you get on your
search in terms of how many hits, and how relevant the
top picks are to what you wanted.
- Try a short string of words or a phrase, such as
"prokaryotic molecular motors" or "DNA-based computer
design". Try inserting Boolean operators ["and",
"or", "not"] between the words to see what effect
they have on your search results. [In some cases, you
will need to capitalize the Boolean operators; in other
cases, you may need to alter your notation.] Add or
subtract some words. Not all search engines work the same
way. Some require specific syntax in word strings. Check
out their "Help" information on advanced searching. This
familiarity will prove useful later on.
Something to consider. How do you evaluate the
quality of the sites found? Say for example you're
looking for information on the latest treatments for skin
cancer. How do you recognize the difference between a
legitimate scientific report on a treatment trial versus
a paper posted by someone with a financial interest in a
particular approach versus something posted by a quack
group? What can you do when performing a search to
maximize useful hits while reducing worthless
ones?
[top of
page]
4. Now that you've had some experience with the
Web and in finding sites of interest, it's time to take a
step back to look at the bigger picture of how it all works.
Try one of the following tutorials if you are unfamiliar
with the structure and function of databases.
By combining what you see here with what you've seen
browsing in your books, you should have a better
appreciation of how the system works as a whole and have an
understanding of what some of the challenges are. This
perspective should prove useful as you progress in the
course.
5. When you access Snoopy in the
Schultz Center's University Library or via the Web, you are
querying the catalogue database. As a way of introducing
databases, the library is a good place to start.
Being able to access current literature is an important
skill in all fields of science. Bioinformatics is no
exception. Browse the following sites to become familiar
with what is available and to become comfortable with
navigating journal databases. It is useful to try searching
for something of interest as a way of testing your search
techniques. This will give you an opportunity to practice
and extend your search strategies into querying databases.
Check your log for ideas of search terms, or come up with
something new. How about finding out what's available on
using BLAST [something we'll be doing next week] or
sequencing genomes [part of Unit 2's focus]? As you
visit each site, make note in your log of the site's
capabilities and uses for future reference. Copy/pasting
information from the web pages is a quick way to do this,
along with citations and your own notes.
When searching database resources from a computer on
campus, you will need to do nothing special to visit
restricted sites. When accessing these restricted sites from
an off-campus computer, you will need to first set up a
proxy, using your library code number as user ID and
select a password [PIN]. If you have never done
this, it is easy to do by using the library's on-line form
available under "info & services". If you already have a
PIN, you need not redo this, unless you want to change your
password. If you forgot your password, you need to visit the
front desk in the library.
For access to Biosis, you no longer need an
additional ID and password to enter Dialog. You can also
access Science Citation Index and Biological Abstracts
through Dialog's portal. Please restrict your uses to
Biological Abstracts, Biosis and Science Citation Index.
Other uses are restricted by contract. Many of the
"off-limits" resources such as Eric and Medline are
available by other means, as you will see. For further
information visit the reference desk in the library.
Why use more than one database when conducting a search?
As you explore, pay attention to what types of resources are
available, the types of journals represented, and how well
you do in obtaining useful titles related to your query.
Knowing what types of databases to use for any specific
query type is something that comes with familiarity with the
contents of the databases available.
How do you obtain hard copies of the papers you find?
This used to be simple. Go to a library which had the
journal [sometimes this required a long trip],
request it or find it on a shelf, queue up at the copier,
and then finally start loading in coins. If you could not
find a library with the journal, too bad. Now, however; we
have many more ways of obtaining full text copies, but that
adds to the challenge of learning the best approach,
prioritizing, and keeping an eye on the budget. Keep this
idea of access and acquisition in mind as you visit these
different sites. Afterwards, reread the paragraph at the end
of this section regarding some things to consider before
establishing a priority path you can use to obtain your
desired hard copies.
- A good place to start is to become familiar with the
tools available locally through the library to find
specific journal papers or journal titles. The library
subscribes not only to specific print versions of
journals, but also to electronic versions of journals and
to databases. [If you simply go looking for hard
copies, you will miss out on a huge variety of resources
available to you.] Go to
http://libweb.sonoma.edu/collections/journals.html
Here you can access Dialog's Biosis,
Elsevier's Science Direct and Wiley's
Interscience, along with other journal
resources, via the Database list. You can use the journal
locator, and connect to New Jour- a full
text resource. Also, periodically check Trial databases
for new things. Note that many of these provide full text
access.
Another local site which is quite useful is the Cell
Molecular Guide: http://libweb.sonoma.edu/research/subject/cellmol.html
- After exploring Interscience through
the library site, try going directly to it:
http://www3.interscience.wiley.com/cgi-bin/simplesearch
See if you find any difference in what you can do and
how you can acquire a copy of a paper.
- In addition to browsing New Jour, a
visit to Highwire Press, the other large
site for free journal access is worthwhile. Both of these
access sites are expanding and adding more journals.
These sites are especially useful after you have found a
citation and you want to check the availability of a
specific journal. Check back for updates so you can
update your acquisition strategy periodically.
http://www.highwire.org/
.
- Next give PubMed a try:
[www.ncbi.nlm.nih.gov/PubMed]
This is the freely accessible Medline, with full text
journal articles available when marked. However, that
does not mean they are all free. Some free ones are
marked as such up front. Others may be free, but you have
to check them out first, since the service providing
access may have different agreements with different
journals. Even if full text availability is not
indicated, you may still be able to get it through some
of the resources you have already visited. It is a good
idea when searching outside of the library portal, that
you utilize your log as much as possible. Collect
summaries and/or abstracts of the articles of interest.
Then you can try different means of getting your hands on
a copy.
- Two other valuable sites to check are
MedBioWorld and BioMedNet.
MedBioWorld is a broad range search site, including
journals and other reference resources. Bio MedNet makes
full text journal articles available, and is the home of
the free e-journal H.M.S. Beagle. [Quick quiz:
What is the significance of the name of this journal?
Who's name is associated with it? Give yourself 2 points
if you are correct.]
[www.sciencekomm.at]
[www.bmn.com]
Now back to the question regarding deciding how to get a
hard copy. If you keep in mind cost, both to you and to a
resource provider, such as the library, then it is fairly
easy to decide how to set up your priority path for
obtaining the articles you want. You might think you
could sit down with you log list of desired papers
and fill out an Inter-Library Loan request for each one,
then sit and wait for days to weeks to get them. Bad idea
for several reasons. Often in the time it takes you to fill
out the form, you could have the paper ready to print out.
If too many requests are made through ILL, the whole system
slows down, because someone else is doing your work for you
while others really needing this service are delayed in
obtaining what they requested. Requests which are determined
to be unnecessary are returned, therefore time is wasted. In
addition, you will need to pay for copies through ILL,
although they are much less expensive when compared to
commercial providers. Therefore save using ILL for when
you can't obtain a paper by another method and you really
need it. For example, you find a paper you want, but it
isn't in the library, it isn't in any full text database you
tried, nor is it available directly from the journal without
a high service charge. What else is there? What about nearby
libraries? A scenic drive might be more desirable than
sitting around impatiently waiting for a pick-up notice in
your e-mail.
[top of
page]
Summary Questions:
Try to limit your answers to 2 typed pages [12 pt
font]. This length should be sufficient for your
comments and any appropriate copy/pasted examples. [You
need not retype or copy/paste the questions as part of your
responses.]
1. Plagiarism has become more of an issue with the
increased use of electronic media and resources. This is due
in part to the ease of access. [It may also be due to
the mistaken assumption that if something is freely
available, it can be used freely without
acknowledgment.] Outline a brief strategy to ensure that
your work is your own and that others receive credit when
credit is due. Give a citation of a useful site you
collected while doing this exercise, perhaps while you were
searching the web. Be sure to use an appropriate style
format.
2. The following pertain to searching the web.
a. Briefly summarize the results of
testing three browser search engines on a general term
and on a word string, with and without Boolean operators.
Include which search engines you used, which terms you
used, the number of hits and their relevance.
b. Discuss how you evaluate the quality of the
sites found. What can you do when performing a search to
maximize useful hits while reducing worthless ones?
3. Briefly summarize your understanding of
databases, including the different types of database and how
they are organized. What do you see as features of key
importance to using bioinformatics databases and tools? What
do you see as key challenges which must be met as this field
grows?
4. The following pertain to searching literature
databases and resources.
a. Outline what steps you took to obtain
a citatation for a specific paper of interest.
b. Outline a checklist of resources and options
to consider in obtaining a copy of a paper in the least
expensive manner, assuming that you don't get it on the
first click from a database. Give an ordered strategy you
would use in the future to guide to you in obtaining
literature of interest in the most efficient, lowest cost
manner. [A one item list of "Ask professor for copy."
is not acceptable! K]
[top of
page]
Further
exploration:
1. If you are looking for interesting resources in
biology & chemistry, try the following:
2. Visit the Tutorial page and explore further
resource links which may prove useful during the semester.
Perhaps you'll even find something helpful for another class
or two.
3. For a preview of 3 major sites that you will be
using in this course and beyond, try exploring NCBI, EMBL,
& Biology Workbench below.
[top of
page]
.
|
|
