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 immunology, 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. 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.] Size the window
so you can easily click on it whenever you want, while
saving most of your screen for the open web browser window.
I like to stagger the corners, so I can easily toggle
between the two windows. 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 the standard on IMACs
and are available on PCs. 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 collect and store references, both from the
literature and for material on the Web. Web etiquette
expects that recognition is given for material found on-line
just as it is expected for books and journals. For
assignments and projects, it is easy to copy/paste onto
another page and then do a little editing. However, care
needs to be taken that the work is your own, and not
plagiarized. Computing exercise 1 provides a basic introduction
to useful sites related to immunology. 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. Computing exercise 2 provides an introduction to
computer-based molecular modeling. Previewing the molecular
model pages at the Kuby interactive site 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.
Following this exercise, I strongly recommend that you
return to the Kuby examples for in-depth instruction on the
details of immunoglobulin structure and antigen-antibody
interaction. 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 3 introduces you to the basic
core of 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.
[That means I started grad school in some prehistoric
era, where sequence gels were fairly new and read manually.
Alignments were also done manually, using a paper-cutter to
cut the strips of sequence data, then taping them together
for alignments. Some poor secretary had to type the whole
mess up.] You will find keeping a log quite valuable in
this exercise. 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. 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 whole papers off the web. 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.
Problems
Keeping a log
Focus of
exercises
Introduction
Focus of Computing Exercises:
The Great Paper Chase
Updated 8/27/04 by thatcher@sonoma.edu