It assumed that everyone in this course has experience in
Web-based navigation. [If not real comfortable, read ch
1 in Baxevanis.] It is also assumed that everone has
some basic experience in using bioinformatics tools, such as
sequence searching, alignments, and modeling. [If not,
or in need of a review, I recommend using the exercises
for Biol 383.] 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: If you are used to
keeping one, fantastic. If not, read the following. 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 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. 1. Browse/read Ch.'s 2, 5, 7 in Baxevanis to get
familiar with file types, retrieval systems, and database
searching. 2. Go to NBIF
and play Origin: Unknown, level 1, to learn more
about BLAST and interpreting results. 3. Go to Biology
Workbench, set up an account if you don't have one, and
browse the site to get somewhat familiar with what is
available and how it works. Tutorials are available from the
homepage- scroll down until you see the link. Biology Workbench is a powerful integrated tool, allowing
you to search multiple databases simultaneously and to use a
very wide variety of tools to examine proteins, nucleotide
sequences, alignments, and structures. The cool thing is
that it can save your work sessions, so you can come back to
them, even months later. You can upload and download from it
as well, so you can easily transfer material to a log, and
to a report. The downside to using Biology Workbench is that
it takes a little practice to navigate following a simple
rule of not using the "back" button, because it can cause
problems.
IntroductionAssignment 1: