[BioSQL-l] Various SQL related stuffola, Protein folding, hello

[Dan Kolis]

Hilmar Lapp   hlapp at gnf.org  said:
>Jim,
>Although MySQL is probably the main platform most biosql-users will 
>use, I know that a fair number of people also run it on Postgres. The 
>shop I'm with is an Oracle shop, so that is the platform I myself 
>mostly work with. If you check out the repository and look into the 
>stuff under sql/biosql-ora, you'll find some things that are probably 
>9i specific, but you may be able to cut those things out to get it 
>instantiated under 8i. We could then document what needs to be changed 
>for 8i.
>As for perl, I'm also the lead developer on bioperl-db, which is the 
>perl language binding for biosql. It establishes persistence for 
>bioperl objects to/from a biosql schema. It's an OR mapper essentially, 
>and so it's no surprise that it's become a fairly complex piece of 
>code. There is a fair number of things to be done for bioperl-db, 
>ranging from documentation to actual code. Just let me know what you 
>want to get yourself into.
>hilmar

Dan says:
Hello. I do electronics but am semi-serious at Genomics, which I did
somewhat before this named concept even existed!

I'm mostly interested in portein folding, and went to CASP3 a while ago. Its
a protein folding conference in California every second year.

Very cool:
http://predictioncenter.llnl.gov/


About the above. For manufacturing support, we use a Visual Basic
application and interface to a linux PostgreSql server, and this is pretty
convienent. If anybody wants the source in VB, its the low level driver with
lots of convienent hooks so the code calling it looks like a series of SQL
and it handles all kinds of details like delimiters, etc so the code is easy
to understand. Of course it could get called by C or whatever, though I
haven't tried that.

Unfortunately, lots of people in every field are used to Windoze so its hard
to institute change. But, just because you use it for some functions, you
don't have to give un linux. And PostGreSql is obviously totally fantastic.

So, if anybody wants it, give me a few days to package it better
documentation wise and I'll email it post it, zip it whatever. Source and
OCX EXE objects, etc. Even if you want to rewrite it or embed PostgreSql
deep into something else, its useful to look as the low level single char
type telnet interface to and from the native PostgreSql process is very
spase and fast, and pretty cryptic.

There are free ODBC drivers, etc all over the place and they are *way* too
slow for any serious work. I got one from I think: Microsoft and it did
about 12 rows a second! You couldn't get through some inquires before the
next ice age with that!

On protein folding... I'm apparently insane as I'm sure only an analog
computer can do anything remotely serious. That's another topic, though

regs
Dan

My Ref:
http://open-bio.org/
http://web.gnf.org/

Dan Kolis - Lindsay Electronics Ltd dank at hq.lindsayelec.com
50 Mary Street West, Lindsay Ontario Canada K9V 2S7
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