[MMTK] Re: [PyMOL] improving interoperability between python moleculetoolkits (fwd)

Konrad Hinsen hinsen@cnrs-orleans.fr
13 Dec 2002 09:50:17 +0100

> One of the reasons I have stuck with OpenDX (www.opendx.org) for
> visualization for so long is the general (object-oriented) data
> model. It has its limitations, but it has proven very powerful.
> Users can define a wide variety of data in hierarchical forms.

Indeed. But this illustrates nicely a frequent problem faced by
software designers: Software like OpenDX is powerful and flexible, but
also huge and difficult to learn. A small specialized tool is easier
to use for the specialized user. Of course those users then find
themselves in a mess of specialized tools a few years later, but it is
rather hopeless to try to warn them about this in advance.

> future system should put a great deal of work into developing a
> strong underlying general data model, not just for molecules, but
> for all kinds of scientific data: grids, vector fields, polygonal
> surfaces, trees etc. Just leaving things open to general objects is

Although that is desirable in principle, too ambitious projects often
end up in either an unfinished or an unmanageable state. Take CORBA,
for example. A great concept, very general but implementations are few
in number, often slow, sometimes expensive, and always come with a
steep learning curve. Or take SGML: the general of the general, but
people started looking at it only when its slim brother XML was there.

It is not easy to find the right equilibrium between simplicity and
generality. For the specific case of scientific computing, I think
simplicity is more important in most cases. Scientists need to
understand and be able to modify code that is the basis for their
research. And they are usually not well-trained software developers.

> Anyone ever checked out the Object Management Group (OMG)? I went to
> one of their meetings (Objects ion Bio- & Chem-Informatics 2001) a
> while back and was impressed with the concept. They are basically a
> non-profit consortium that sets open industry standards for objects

Well... It's a design by committee approach that has rarely produced
useful results in spite of an enormous effort. Moreover, which
scientist can afford to participate in their meetings? That's a
full-time job.

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