[Pipet Devel] links

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Nov 23 15:42:30 EST 1998

> I did some searching for applications that might be helpful for us to
> take a look at.  Below are links to sites about algorithms that may be

Thanks, that's a useful list to have!

> So far, I have found _no_large_bioinformatics_package_with_GNU_GPL_code_!

No surprise, GPL isn't really common in the scientific world.

> to be GTK/GNOME. However, this alone would restrict all tools for
> TULIP to be written in either C or Python.

No, just in languages that are linkable with C, i.e. almost all!

> From my experience, more than about 50% of the algorithms (written
> by others) that we might want to implement are written in FORTRAN.

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).

> Pascal. To deal with this, we may want to use two very powerful
> modules/tools for tying together different languages: Expect and
> CORBA. Below I pasted something I just put up on the TULIP Web site:

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). 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.

>     Low-Level Communication Via Fnorb (CORBA).  Fnorb will allow for
>     better communication between tools, meaning more control.  This

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

> Also, check out what I wrote about using a "Glyphic Command Language"
> for the workspace:
>    http://www.uml.edu/Dept/Chem/UMLBIC/Apps/TULIP/model.html
>    (bottom of the page)

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?

Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
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