[Pipet Devel] Re: [pyphy] Mavric Tk version

[J.W. Bizzaro]

(from pyphy; CC to pipet-devel)

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://bioinformatics.org/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 at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
--