This post originated from an RSS feed registered with Python Buzz
by Andrew Dalke.
Original Post: Site changes
Feed Title: Andrew Dalke's writings
Feed URL: http://www.dalkescientific.com/writings/diary/diary-rss.xml
Feed Description: Writings from the software side of bioinformatics and chemical informatics, with a heaping of Python thrown in for good measure.
I've been revamping my website over the last few weeks. It's been
slow going, in part because there are a lot of behind the scenes
changes. The site is a set of files; there's no server except for
Apache. I could install a server, but the machine is hosted by Pair.com and running a server would
cost more, which wasn't warranted for a static site. When I updated
news items or released a software package, I made a copy of the
template and modified everything by hand. Tedious, but it was only
done every three months or so.
That's changed, as you can tell. I'm using the site more as an
advertising medium, so people will know about my company and what it
does. (If you want to hire us, contact info@dalkescientific.com.)
I replaced the hand-written templates with a templating system based
on
ZPT
(more specifically, on
SimpleTAL
and a highly modified version of
PubTal).
It took a while to get running, in part because I used it to
experiment with new ideas, include ZPT. I also have a good idea now
of how to write a Pythonic plug-in system, and tried out a few
of the more obscure modules, like multifile (Hint: not worth
it.)
Were I to do it again -- something I don't look forward to -- I would
host Zope locally and write some code to export the relevant pages.
Then again, someday I'll set up a server. That'll even let me have
these "trackbacks" I read about. But since I read web pags and send
emails, I still haven't drank that flavor-aide.
The next stage is to support RSS feeds. I looked around and didn't
find any good code to generate RSS. The ones I found either didn't
handle proper escaping, were incomplete (then again, most people don't
need RSS), or just treated RSS as a generic XML and/or RDF. I wanted
something which acted like Python objects. So I wrote PyRSS2Gen. But it probably won't be
finished for another few days as I'm going to Michel Sanner's
Computational Representations of Biomolecules workshop at UCSD
followed by SciPy at CalTech.
I'm really looking forward to Michel's conference. It's something
I've been interested in for many years. My first "computational
representation' of a biomolecule was in 1992 when as an undergrad I
helped write a parallelization of CHARMm for Paul Bash and since then
I've been a major contributor to
VMD,
NAMD,
PyDaylight and been involved with
(either as contributor, user, or simple kibitzer) for frowns,
OEChem, Tripos (they have some thoughts about using Python!),
and others. Even more if you talk about software I've used
which is based on molecules but where I haven't seend the API.
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