[kepler-dev] an introduction and some questions

Timothy McPhillips tmcphillips at mac.com
Mon Apr 4 14:26:00 PDT 2005

Dear All,

I have been lurking on kepler-dev for a while and thought now was a 
good time to introduce myself.

I am using Ptolemy II for automating scientific workflows in 
evolutionary biology (e.g., inferring phylogenetic trees).  This work 
is central to the Natural Diversity Discovery Project, a non-profit 
organization I am founding.   One goal of the NDDP is to make it easy 
for the general public to access the latest scientific data related to 
evolutionary biology and to help the public understand the implications 
of this data.  (You can read a bit more about this project on the 
single web page I have up at  http://www.naturaldiversity.org.  I plan 
to expand the web site shortly.)

I talked with Bertram Ludaescher and Shawn Bowers last month.  Bertram 
suggested that I contribute the NDDP actors to the Kepler project, and 
Shawn has sponsored me for a CVS trial account.  Before I add any files 
to the repository, I wonder if I could get a little more information 
about Kepler:

1.  Would it be OK to create a Kepler software release customized for 
NDDP users?  (I mean direct users of the "phylogenetics workflow 
automation framework," not those using the web-based "discovery 
environment"--see the NDDP web page).  The variety of actors in Kepler 
and Ptolemy II is rather dizzying.  I'd like to keep things simple for 
my users (and keep the software distribution reasonably sized).

2.  Are there procedures for determining and documenting the stability 
and quality of code, e.g., something like the Ptolemy project's code 
rating system?  And are specific people or groups responsible for 
maintaining particular sub-projects or source files?  I'd like to have 
some way of knowing that only stable, tested code makes it into NDDP 
software releases. And it would be nice to know who to turn to if a 
problem arises.

3.  Are there any policies (or strong feelings) on intellectual 
property and software licensing?  I see many Kepler source files that 
are copyrighted by the University of California and have a 
Berkeley-style license.  I also see a fair number of files with a GNU 
Public License.  I want to be able to distribute NDDP software freely 
(I've used an MIT-style license for past projects). I would like the 
NDDP to retain the copyright on the software I contribute.  And I would 
prefer to avoid dependencies on software with licenses more restrictive 
than the Berkeley license.  Does using a CVS repository at UCSB (?) 
have any implications in these regards?

Thanks very much for any help you can provide.  I know from experience 
that these kinds of organizational issues can be time-consuming to 
address.  Be assured that I very much admire the Kepler effort and hope 
that I can contribute to it.

Best regards,

Tim McPhillips

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