[seek-dev] implementing garp in ptolemy

Rich Williams rwilliams at nceas.ucsb.edu
Fri Nov 7 14:17:25 PST 2003

Hey Chad -

Are you are working off Deana's workflow figures?  In Santa Barbara, we
refined one of those workflows considerably, including specifying inputs and
outputs to various steps.  Check out
ut.ppt, though it probably needs some more explanation to be useful to you.
There's a presentation at the start of the file that ends with a 'what's
next' slide, and then there are detailed ins and outs of various steps.

We spend some time discussing the appropriate level of granularity for the
pipeline, and decided that Deana pretty much got it right.  For example, the
step of taking the layers of species occurrence and environmental properties
and producing the data set used later in the GARP analysis is potentially of
interest to other users and so should be separated out as a reusable step.
In the powerpoint presentation that step is called "Dave's presample
process".  Similarly, value was seen in separating the GARP rule computation
from the projection that uses the rules, as the various different flavors of
the GARP pipeline all use the rule generation step.

All this of course will require some coding work to refactor the existing
GARP code so that these separate components are appropriately isolated.  I
don't know whether that is a practical engineering task, and perhaps an
initial implementation that doesn't try to re-engineer the existing code
would be in order.

I'm certainly available to discuss the work we did on this in Santa Barbara.
I think I now have a decent understanding of the semantics of the inputs and
outputs of the various steps and therefore of the work going on inside the
various steps.


> -----Original Message-----
> From: seek-dev-admin at ecoinformatics.org
> [mailto:seek-dev-admin at ecoinformatics.org]On Behalf Of Chad Berkley
> Sent: Friday, November 07, 2003 12:12 PM
> To: Ricardo Scachetti Pereira; Deana Pennington; Matt Jones; Dave
> Vieglais; seek-dev at ecoinformatics.org
> Subject: [seek-dev] implementing garp in ptolemy
> Hi All,
> I've been looking at trying to get GARP working in ptolemy a bit, and I
> have a few questions.  First of all, is the modularity that is described
> in the PPT files the modularity that you would want in a ptolemy model?
>   for example, is the "data calculation" step in the "GARP Native
> Species Pipeline" something that you would want to reuse in other
> pipelines?  When I talked to Dave when we were here in SB, I got the
> impression that he thought GARP should just be one atomic actor (is that
> really what you think Dave?)  If these components are never going to be
> reused for any other pipeline, then they should probably just be folded
> into one generic GARP actor.
> I'd like get together, either physically or virtually, with someone that
> can explain to me the exact steps that it takes to go from the training
> data and layers to output.  The specifications of the modules within the
> PPT documents are a bit vague.  For instance, I have no idea what data
> calculation does.  A mid-level pseudo-code implementation of GARP might
> be a good idea, as it would help me get my head around this thing a bit
> more.
> Could any of you have a phone call next week?  maybe wednesday since
> tuesday is a holiday?
> chad
> --
> -----------------------
> Chad Berkley
> National Center for
> Ecological Analysis
> and Synthesis (NCEAS)
> berkley at nceas.ucsb.edu
> -----------------------
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