[Pipet Devel] links

J.W. Bizzaro bizzaro at bc.edu
Mon Nov 23 16:59:31 EST 1998

Konrad Hinsen wrote:
> No, just in languages that are linkable with C, i.e. almost all!
> No problem. I am using Fortran routines called from Python regularly.
> The only complication is that C/Fortran linking is machine dependent,
> which makes automatic installation difficult (but not impossible).

Great!  I'm glad to hear you have experience with that; we'll need it.
Automatic installation on various platforms will not be easy especially
considering all of the libraries we will be using!

> Expect is a bit of a kludge, but I agree that it can be useful for
> really weird programs (i.e. Pascal or Java, or binary-only
> distributions).

Exactly.  I was considering (1) weird languages and (2) binary-only,
especially for non-core tools that someone may want to sell or have
the code kept hidden.

> CORBA would be useful if there were programs with
> CORBA support that we want to call, but I'd be surprised if that were
> the case! Modifying these programs to use CORBA sounds like an
> extremely unpleasant task.

I think CORBA is becoming much more popular now.  GNOME is
a good example, which uses ORBit...GNU(?) CORBA.  But, if you
think it is not necessary, we will hold off on it.

> Fnorb has one problem: it is not free for everyone, just for
> non-commercial use.

I did not know that.  Hmmmm.  That rules that out.

> > Also, check out what I wrote about using a "Glyphic Command Language"
> > for the workspace:
> An interesting idea. Unfortunately I know much too little about the
> applications we are aiming at to judge how useful it would be!
> Could you give some fictitious example?

Well, I was considering it for the workspace, which I see as virtual
laboratory benchtop where you can organize your equipment (tools) and
specimens (data).  It won't matter what the tools and data are, GCL is
just a way to organize them and generate a flow-chart for the experiment

The important features of GCL are (1) being able to form an input dialog
with a tool.  For example, "SEQUENCEALIGNER--ALIGN--SEQ-(to)-DATABASE".
You see, this can be represented as 4 glyphs on the benchtop.  And if
you represent all 4 together as a single glyph, you can then start forming
classic UNIX-like redirects and pipes, etc.  In other words, you can do
more than one thing with a single "line" of commands.  It may be just kind
of cute for one-shot analyses, but if you have an analysis that will take
days, why not have TULIP go ahead and do something else when it finishes
at 3:00AM Saturday morning? :-)

J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/

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