[Bioperl-l] Initial draft of bioperl tutorial committed

Peter Schattner schattner@alum.mit.edu
Mon, 08 Jan 2001 11:44:08 -0800

Hello all

I have committed an initial draft of an introductory bioperl tutorial
(called "bptutorial.pl") to the bioperl-live (main) repository.  The
draft tutorial pretty much follows the outline from my proposal:
One addition to the original proposal is that I have included an
"appendix" which is a working script that demonstrates most of the
bioperl features described in the tutorial. (The script is largely
cut-and-pasted from various test and example files with print statements
added to make it clearer as to what is going on).

I believe that having a clear and accurate tutorial could make bioperl
more accessible and widely used.  On the other hand, if the tutorial is
confusing or contains mistakes, it will turn people away from trying
bioperl (and probably be worse than not having one at all).   So I have
a request.  I would appreciate it if some of you would read the tutorial
and give me feedback in terms of clarity and accuracy.  I am interested
in both general comments (eg "this section is too long - cut out
such-and-such" or "this module description fits better in this section"
or "this module will not be included in the 0.7 release so don't include
it" ) and specific places where there are errors or misleading or
confusing statements.  (If you think that the tutorial is clear and/or
that specific parts are particularly helpful I'd of course be happy to
get that feedback too :--).  Suggestions on improving the formatting
would also be appreciated.

I would definitely like feedback from people who have written modules
which are in the 0.7 release to make sure that I have captured your
intent and the proper usage of your module(s). I would also like
comments from folks who are simply bioperl users and, ideally, from a
few people who haven't used bioperl much before to see in what ways the
tutorial makes it easier to use or get started using bioperl (or
doesn't).  Feel free to write to me directly at schattner@alum.mit.edu
or via this list.  Thanks.

If you just want to look at the tutorial, you can view it through the
web browsable CVS at :

(Note: you may need to view the tutorial through a word processor to get
the lines to wrap properly and to get rid of extra '^M's.  If someone
can tell me how I need to reformat the file so this is not necessary I'd
be grateful.)

If you want to also run the tutorial script, you will need to have a
copy  of CVS "bioperl-live". The tutorial script will *not* work with
release 0.6. (Note that the contents of bioperl-live are being updated
often so some of the demo scripts may fail - they're working for me now
and if they start failing I'd appreciate finding out).