[Pipet Devel] Re: pDRAW and Loci

[J.W. Bizzaro]

Kjeld Olesen wrote:
> 
> First of all I should say that, yes, I am interested
> in contributing to your Loci suite.

Great!

> Secondly, I should inform you that pDRAW is programmed
> using Visual Basic. Although I have been using both
> Turbo Pascal and Delphi at some points, and I can make
> basic Javascript programs etc etc, you would
> probalby consider me an inexperienced programmer.
> At least I do not have any experience of C and only
> limited experience with UNIX/Linux.
> This could change of course

That's okay.  I started out with true BASIC back around 1981, and then I learn
Pascal in college, which turned out to be somewhat useless (just after I learned
it, everyone started switching to C).  I did a bit of programming in Delphi
recently, which made some use of my Pascal skills.  I am still rather new to C,
and now I'm learning Python, which will also be used in Loci.

So, welcome to the club :-)

> Thirdly, I'd like to know some more details of what would be
> required of the plasmid drawing plug-in for Loci?
> Will this plug-in also have to do the analysis of the
> sequence, or will the analysis data be feed from Loci?

The model is being refined as we go along, but a "plug-in" is split up into
several parts.  The first thing I thought you might want to do is make a
high-level widget for drawing plasmids, like what you have done for pDRAW.

Analysis routines are separate from all GUI's, which is a key feature of Loci. 
They will be wrapped in a set of Python modules that connect the analytical tool
to the rest of Loci.  These modules will be cutomized to translate user_input ->
analy_tool_input and then analy_tool_output -> output_to_user.  Plus they will
communicate with a central workspace for monitoring.

> Apart from drawing, will the plug-in also have to be able
> to print and/or provide some sort of metafile for the clipboard?

Ah, yes.  Loci also acts as a drawing program for scientific publications, so
the drawing widget itself should be able to output some graphics format.  I
think Postscript may be best.  The output from the drawing widget will be
transferred to a drawing program.  Several drawings can then be combined, and
the user can add text and additional graphics.

> What will be the anticipated milestones for the Loci project?

I'm sorry things are so sketchy right now.  It seems that everytime we try to
pin down a design, we come up with some more ideas, and of course things change
as we see how well or how poorly features can be implemented.

I would say that each major component of Loci is a milestone.  So, we need (1) a
GUI system (which I just started, (2) drawing widgets (one of which I hope
you'll help with), (3) the server/app-broker system, (4) wrappers for plug-ins,
(5) workspace and drawing tools (also plug-ins I think), and (6) basic plug-ins
that can do analyses.

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Kjeld, where are you from?  One of the developers is in Sweden.  I wondering
because your name sounds Scandinavian of course.

Let me know about setting up a Linux shell account for you on the system, if
you're ready for one.  Also, let me know if you need any tips on C and Python,
where to get more info.


Cheers.
Jeff
-- 
J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
--