If you want X, you know where to find it (was Re: do...until wisdom needed...)

[Douglas Alan]

"Andrew Dalke" <dalke at acm.org> writes:

> Douglas Alan:
>> What's "structural biology"?

> Biological systems are made of molecules like proteins, DNA,
> RNA, lipids, sugars, water, ions, etc.  These are physical objects
> in a 3D world.  Structual biology studies those types of molecules
> with a focus on understanding how they physically interact.

> For pictures from my old research group,
>   http://www.ks.uiuc.edu/Overview/gallery/structure.shtml

Very cool.  Thanks.

>> One of my oldest friends has just finished writing one of the
>> first textbooks on computational biology.

> I'm confused (again :).  There are quite a few books on
> computational biology.

Hmmm, well maybe he said one of the first textbooks on "_______
Computational Biology", where I've forgotten what goes in the blank.
In any case, here's a pre-publication review of his book:

     "This is a very timely book on the statistical foundation of
     bioinformatics. There are already many excellent books on various
     topics in computational biology and bioinformatics but none of
     them is self-contained with respect to the statistical treatment
     in the sense that necessary background on probability and
     statistics are provided and integrated with the development of
     specialized bioinformatics topics such as BLAST and HMM.  The
     treatment on BLAST theory is especially appealing and is not
     available in any other book that I am aware of. The authors first
     developed with care the background probability theory (extreme
     value theory, excursion of random walk, sequential trials, etc.),
     and then apply them in elegant manner to the BLAST theory." (Wing
     Wong, Harvard University)

> I have written converters from other languages into Python and
> used the f2c model of converting the code into actual Python
> source code.

What kind of languages?

> My point is, existing tools don't quite handle Python's syntax
> without some coercing, so making things more powerful (eg, with the
> ability to define macros, new keywords, etc.)  makes those tools
> even harder to write.

That's true.  Gotta keep those tool-writers on their toes though.

This is something of an issue in Lisp too, though Lisp is much easier
to parse.  When you use Lisp-mode in Emacs, you have to tell Emacs
what macros you are using and how you would like them indented, or
else you have to indent them manually.  With Python-mode, I think the
biggest probem would be that Emacs wouldn't acurrately highlight
keywords within a macro invocation.  It will end up highlighting words
that shouldn't be and not highlighting words that should be.

|>oug