[Pipet Devel] PAOS and the Work Flow System

J.W. Bizzaro bizzaro at bc.edu
Tue Apr 13 15:14:06 EDT 1999

Humberto Ortiz Zuazaga wrote:
> bizzaro at bc.edu said:
> > There are more updated terms for what Carlos says below:
> > Gnome clients == Benchtop + FigBuilder
> Carlos seems to mean any GUI locus.
> > Tool Manager == The part of a
> > viewer (or maybe a separate process) that communicates via the WFS.
> No, I think Tool Manager == analytical locus.

Perhaps you are right :-)  There was some confusion early on that the Benchtop
communicated only with remote analysis loci.  It of course communicates with
viewers too.

In any case, all loci it seems will need a "Tool Manager" component for

> If PAOS won't shuffle data around, we'll need another mechanism for getting
> data into an analytical locus.  It will have to be able to contact remote loci:

>From and earlier message:

    PAOS -> for active communication about the internals of Loci
    XML  -> for archiving and translating bio data AND LOCI INTERNALS

But to make a complete WFS, I have been saying that we need an XML parser to go
along with PAOS.  Of course I want the WFS to be a seamless system.

> I fire up my seqence editor, type in a few bases from my still wet autorad,
> and click on the blast button.

call SeqViewer -> call SeqEditor -> type bases -> updated to SeqViewer -> close
SeqEditor (optional) -> at Seqviewer pull down menu with optional analyses
(known to local AppBroker) -> select Blast...

> The sequence data will have to be transfered to the remote blast locus.
> The python XML topic guide at:
> http://www.python.org/topics/xml/xml.html
> lists two proposals for an XML over HTTP RPC mechanism, this or something
> similar can be used as loci's "transfer" mechanism (in the sense transfer is
> used in the glossary). These particular proposals seem a little too low level
> (they define a XML for bytes and integers etc), but the basic idea of using
> XML to transfer data and specify a remote procedure call syntax seems like
> what we need.

I'm not sure what transfer protocol PAOS uses over an Internet socket.  Carlos? 
But we may not be looking at HTTP.  So, probably something "similar".  PAOS
should be in control of this file transfer to some extent.

J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/

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