[Pipet Devel] embedding queries in XML

J.W. Bizzaro bizzaro at bc.edu
Sun Jan 24 21:25:40 EST 1999

Harry Mangalam wrote:

> the use of an i/o language called boulderio which
> had its beginnings in development of the Whitehead's 'Primer'.  He described
> it as a way to pass data thru pipes with each added analyses being able to
> tag it with additional info. I'm not suggesting using it as is, but the idea
> of being able to add analytical value to a pipes/streams-based dataflow is
> vary attractive, especially to a large effort such as a genome initiative or
> even pharma.
> This is a lightweight approach to marking up data so that it can be passed
> from app to app.  It is not a very formal approach, but it has been used to
> coordinate some very large sequencing efforts.

I like what was suggested by someone on the team earlier, that the XML file
can contain a list of queries to be performed and already performed.  In that
sense, the XML files say "This is where I'm going.  And this is where I've
been.  Can you help me?"  So if the player who catches the basketball doesn't
know where to throw it to, he can read the name of the recipient and sender
right off of the ball.

Why would a locus get an XML file it wasn't intended to get?  Maybe this idea
is best suited for a router system.  Can each locus be a router?  Each one
_should_ be.  Even if a locus was intended to get the data and do something
with it, if the next step is to send the data somewhere else, it should know
where to send it.

Maybe the list of queries/commands can be put into the XML from the GCL
Benchtop, at the start of the analysis.  This way, the GCL won't have to
control every step.  Each locus won't have to ask the GCL where it should go
next.  The XML data will know the path.

Once again, I'm not sure how this would work with Paos.  Can you enlighten us
Carlos?  Can an XML object be treated as a mobile object with a mission?

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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