[pyphy] Mavric Tk version
J.W. Bizzaro
bizzaro@bc.edu
Wed, 05 May 1999 15:29:44 -0400
(from pyphy; CC to loci-general)
Rick Ree wrote:
> > Jeff:
> > How should we refer to Loci/pyphy/mavric when using loci generated tree
> > pictures in papers ?
Thomas, I'm not sure what you mean by "refer". Are you talking about a
reference for a printed journal article? Loci probably won't be generating its
own pictures for a while, which leads to Rick's question below.
> A related question: is 'pyphy' the same as 'inst-phy' (listed as one of
> the components of Loci on the web page)? If so, then maybe we should drop
> the name 'mavric' and consolidate it all under one name.
For Loci, an "inst" is an "instrument", which is essentially a plug-in to the
Loci system and not a stand-alone program.
> Also, could someone clarify for me the relationship between the Loci
> system and its components -- i.e., are the components just stand-alone
> apps that use Loci code, and can communicate with other Loci components?
No, components, mostly what we've been calling "loci" or "locuses", are
plug-ins. Although it should be possible to make a stand-alone that interfaces
with Loci, we will be focusing on accommodating plug-ins.
I have been putting together a "tour" of the system. It has no text right now,
but a plug-in would start out as a non-GUI "Instrument" and make direct use of
(even customize) the "Instrument Panel" and "Slide", which are the GUI
components:
http://theopenlab.uml.edu/loci/tour/index.html
> I'm a little confused. Can I write an application using pyphy code and
> call it 'mavric'? (It's silly, and shamelessly self-promoting, but I kind
> of like the name :)
If by application you mean plug-in, yes. But pyphy and mavric would have to be
modified quite a bit. You see, Loci is designed to give a GUI to command-line
programs, so you would have to take the non-GUI parts of pyphy/mavric, and make
an "instrument". You would then have to specify the GUI: the "instrument panel"
for user input and the output that goes to the "slide".
As I mentioned above, you could turn pyphy/mavric into a stand-alone that
interfaces with Loci, and that may be less work. I don't have any problems with
a stand-alone "pyphy/mavric" (I'm still confused about that name :-) that is
separate from Loci (not every TOL project has to run under Loci), but I do
intend to have an "inst-phy" (phylogenetic instrument) that is a plug-in as part
of the Loci core (very basic distribution).
Gutten whatever.
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
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