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Subject: Comments on draft outline
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Course faculty, developers et al.,

I've signed on to this course as a student and, although I haven't been
participating in the development of the syllabus and chapter outlines, I
have been following the listserv postings.  Now having read over the
drafts of the course outline and various chapters, I have these general
comments to offer:

Introd (Ch. 0): I agree that it is useful to cover the rudiments of
molecular biology (RNA, DNA, etc.), but what is helpful here is the
author's perspective and insights (for example, on the controversy over
the use of BLAST vs. FASTA).  The more of this that is provided up front
in the course the better since such information will clue students into
what they should pay attention to.  Picky style point: all capitals
(LIKE THIS) should not be used for emphasis in the text (the sequence
databases are described as "HUGE"); there are simply too many
abbreviations and acronyms floating around in this field and the risk of
confusion is too great.  Better to use boldface or underlining.

PrwAli (Ch. 1): Looks good.  I suppose that gapping will be discussed in
Section 1.1 under global alignment.  Since this is such a critical issue
in sequence analysis, perhaps it deserves a reasonably detailed
treatment?

Netwkg (Ch. 2): Enormous topic and my congratulations to David Steffen
for his admirable first cut at it.  Perhaps Biological Abstracts
(BioAbs) should be discussed together with Medline, ENTREZ and OMIM. It
appears, and I am hopeful, that explicit instructions on the use of the
various resources will be provided.  This will make the chapter
invaluable in its own right, far beyond the use intended in this course.
Ditto criticism of ALL CAPS for emphasis (e.g., "THE Internet").

MathAn (Ch. 3): In deference to the importance of the mathematical
foundations of sequence analysis, perhaps section 3.2 could receive
greater emphasis (more than the 5 of 20 sections proposed).  While I
think the emphasis on the practical applications of phylogenetic
analyses and use of examples (including the proposed homework) is
outstanding, I believe that the mathematical theory is also important to
understand for purposes of developing improved methods.  Perhaps this
concern could be addressed by the inclusion of pointers to useful
references for those who would like to know more.

MulAli (Ch. 4): Another enormous and important topic.  The draft outline
is excellent and appears to aim for an appropriate level of detail.
Like section 3.2, above, the theory of multiple alignment is critical to
the understanding of numerous useful applications of sequence alignment
tools.  Again, good references here will be essential.  Homework and
problem solving will be critical for learning this information, thus it
 will be useful if the homework will involve "lower level" problems, such
as analysis of critical algorithms, in addition to some multiple
alignment problems.

ProtEn (Ch. 5): Looks like fun. This section reflects the fundamental
principle that in light of the breathtaking pace of technological
development, we, as practitioners of science at all levels, must take
into account the likely future even in our relatively short-term plans.

Generally:
  Homework:  Assignments that use real-life examples culled from
research and primary literature are valuable in that they can teach
basic principles as well as demonstrate their application.  I hope that
there will be some emphasis on these in the homework problems.

  Level of technical detail:  Everybody has been very sensitive to the
issue of not teaching at a level of technical detail that is beyond that
of the average student.  That is a good attitude to have.  However, as
this course is in some sense, to twist the cliche, "teaching to the
converted," most students will likely have either some background in
math and comp sci or will at least be accustomed to learning technical
and analytical information.  My hope is that the course will fearlessly
endeavor to teach the technical aspects of biocomputing in order to help
us students contribute to the development of better methods and software
tools rather than merely becoming expert users.  In this regard, it will
be helpful to provide good references to standard texts or papers in
the field in the case that we need to bone up on an unfamiliar topic.

Lastly, to David Steffen:  I tried to email Georg a beer, but it got all
over my keyboard; I ended up having to drink it.  Could you please
explain your beer-email facility in your Networking chapter?  I'm sure
we all would find that very useful.  I even volunteer my address for
people's practice.

Thanks to all for the hard work and thoughtful consideration you are
investing in the class.  Please let me know if I can be of any help.

Regards,

  --Mykol

------------------------------------------------------------------------
Mykol Larvie                                        mykol@mit.edu
                                            mykol@rascal.med.harvard.edu

         Maintain separation of church and state --
                 support a moment of silent masturbation in school