[Pipet Devel] inter-locus communication

J.W. Bizzaro bizzaro at bc.edu
Tue Mar 16 17:11:33 EST 1999

Rahul Jain wrote:
> In the plan I gave you guys, I only meant for the XML to be a way to
> communicate between a wfs and the Workspace (GUI).

I don't see WFS <---> Workspace (Work Flow Diagram and Notebook) communication
being much different from WFS <---> Tool communication.

> It was designed so that
> intermittently connected clients (or people who need to log out) can check
> up on the status of their analysis from time to time, esp. on a really
> long analysis.

I like this idea.  Was it Justin who first suggested it?  It's a good argument
for keeping a "hard copy" of the workflow data on disk via XML.  Imagine that
the system goes down for some reason, or even that the user wants to exit Loci
and log out.  Loci could just pick up later where it left off.

> Regarding the comment on making workflow information independent from the
> biological stuff, I think the data section covers that separation quite
> well. Keep the bio-related stuff in between the <data> and </data> tags
> and the rest is Loci-specific workflow information. This format also makes
> it easy to store the results of an analysis for archival purposes.

This is from your message:

    [data block]
    <step id="q1">
      [data block]
    [more steps]

Let's see..

<data> is either workflow or bio
<input> and <output> are workflow
<step> is workflow
[data block] is bio

If that is correct, bio data is nested directly in workflow sections in 2
cases.  I suppose this is acceptable if the definition of BICML will allow for
bio data to go directly under <data>:

  <aa1d id=12378728937>
    (amino acid 1-dimensional/sequence)

Something like that :-)

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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