To those of you who have already embraced the Information
Age: You should find that the web-based instructional
support and learning activities will be a fun enrichment to
the course. To those of you who have not yet driven the Information
Superhighway, or only tried it a few times: You may find
some of this intimidating at first. However, after exploring
these pages and working through the exercises, your comfort
level will increase. The secondary gain will be that as you
gain expertise in virology, your computing skills will
increase as well. To all: Problems will occur.
Links to specified sites may change. A page on this site may
not load properly. Unique problems may surface associated
with specific server access. An analysis application may
crash or give consistent error messages. Whatever it is,
please communicate- both with me and with your fellow
classmates. The first forum topic I have posted [click
on "Interactive", go to "Discussion Fora"]
is titled "Computer problems". If you have a problem,
make a posting. Check the forum frequently. If you see where
you can contribute a solution, please do. You may find an
answer to your problem in someone else's posting. If the
problem is associated with a campus computer, or if you
think it may be due to the SSU server, or even if you are
not sure, try the help line: 664-HELP. Keeping a log: It is easy to get
caught up in surfing the web, but how do you keep track of
all the places you'd like to come back to? How do you
minimize the time spent and maximize the information
retrieved? How can you be sure that you recorded the URLs
[Internet addresses] correctly? How can you speed up
the process? The answer to all of the above questions is to
make and use a log. A log is an incredibly handy tool and quite easy to set
up. Open a page in your favorite word processing program or
notepad. [I recommend a recent version of Word, because
you can automatically turn URLs into active links by using
return/enter at the end of the address.] It is easy to
toggle between windows or to size them to see more than one
at a time. Experiment a bit to find a system you like. When you find something you want to save, be it a single
address or a whole page of information, you can simply
copy/paste between the browser and your log. You can add
your own notes and comments as you go, note questions you
have, ideas you want to follow in the future, and so on. Be
sure to save your log to a disk. If using school computer
labs, the log has an additional advantage for bookmarks.
Since bookmarks are regularly removed from lab computers,
the log allows you to carry your bookmarks to any machine
you want. [Note: Zip drives are becoming the standard.
Some machines have 100 MB drives and others have 250 MB
drives. Both types will read/write on 100 MB, so that is the
best size of zip disk to get.] The log can be advantageous for completing assignments.
Besides editing them for your own use and making them
functional accessories to surfing, you can use them to store
material for answering homework questions and for projects.
It is easy to copy/paste onto another page and then do a
little editing. A word about printing: If using on-campus
computers in computer labs, you only need to provide your
own paper for the printer in the lab, or you can e-mail
stuff home to print on your own printer. If using computers
in the library, you can either pay ten cents/page or you can
use e-mail, which is cheaper. Computing exercise 1 has two main objectives.
First, it provides a basic introduction to useful sites
related to virology. In addition to providing sites, there
is instruction on how to go about finding sites of interest
by using search engines. Developing efficient search
strategies early will help in many ways throughout the
semester, and beyond. I encourage everyone to extend beyond
the limits of the exercise by exploring some other links
given on the "Links" page. Second, it provides an introduction to computer-based
molecular modeling. Previewing the molecular model pages at
the Kuby & Lodish interactive sites will give you a
taste of what you can do. In the exercise, instructions are
given on how to find and view molecular models of proteins.
As we progress in the course, you may find it useful to look
up the structure of some of the specific proteins
discussed. Computing exercise 2 introduces you to the basic
core of molecular bioinformatics, which includes locating
specific nucleic acid and protein sequences, searching for
homologous sequences and making alignment maps, and looking
for homologies among a selected group of sequences. The
power of computers and quality application programs have
made these tasks quite simple when compared to what could be
done just a few years ago. This is an area where a "long,
long time ago" and "once upon a time" means only 10-15
years. You will find keeping a log quite valuable in this
exercise. Computing exercise 3 is your chance to utilize
what you have learned in the first two exercises and apply
it to a topic of your interest. This is intended to be a
short project using bioinformatics tools and techniques to
answer a question related to virology. You need to design
your project, find the data, run the analysis, and write a
short report. After all three exercises are completed, there will be a
survey on this portion of the course. You will earn
points for completing the survey, but the content of the
survey results are anonymous. I will use the results to
improve future offerings of the exercises. Access to these exercises can be done either by
using the links at the top of the page, or from the index. I
recommend using the exercise on-line; that way, you only
have to click on the active links. However, they are set up
so that you can print them out, and manually enter the
URL's. An alternate approach would be to copy the contents
of the exercise into your log, then just work from one
browser window and the log. This is advisable if you have
limited RAM or if you have problems running multiple
windows. Although a separate assignment not focused on
bioinformatics per se, the Paper Chase does require computer
search tools and strategies. The primary search resource for
this is PubMed, available through NCBI. Other literature
search engines are available to you as well. Use of a log
here can save time while hunting for listed citations or in
making requests for copies of specific papers. You will also
learn how to search for on-line journals and to directly
download full-text papers off the web. On the second day of class, you will be given your ID and
password. You may change your password to suit your needs.
You may also select a global ID and password, if you have
several WebCT accounts, which is easier than trying to
remember several passwords. To do that, go to the WebCT
homepage. You will have the opportunity to exchange news and views
via the course email [like a list-serve] and in
discussion fora. If your study group wants on-line access,
that can be arranged. For a general guide to using WebCT, go to: Check back here for updated information regarding tips,
tricks, and changes specific to this course. Announcements
will be made on the homepage to let you know if there is
something new.
a
IntroductionFocus of Computing Exercises:
The Great Paper Chase
Interactive Virology Using WebCT
http://www.sonoma.edu/people/cochran/edu480/webct_guide.html
Updated 3/4/02 by thatcher@sonoma.edu