Subject: Re: CCL:RE:Anybody agrees with me

From: [email-masked]
Date: Fri, 11 Feb 2000 12:37:45 +0100

> In my opinion there is two life sciences area of applications that 
> currently need standards:
> 1) GUI
> 2) Methods
> 
> This sounds to me like classes in OOP.

Well, yes, but it's not that easy...

> 1) Hence we can focus on developing standard classes for GUI that
> will inherit all the properties needed for a particular application.
> This will leave room to every developer to adapt its GUI to its own
> program.

This has been going on for quite a while now. There are dozens of
GUI libraries, each of which claims to be standard, portable, etc.

I don't mean to say that GUI libraries are useless. They make using
GUIs a lot easier. But it seems that standardization is still in the
remote future.

> 2) About methods such as force fields, we can for example develop a class 
> call force fields that will implements all the basic information that make 
> up a FF. This will leave to the developers the opportunity to expand 
> its method while inheriting basic components.

This is exactly the approach I have been following with my OpenSource
simulation library, the Molecular Modeling Toolkit
(http://starship.python.net/crew/hinsen/MMTK/). In my experience, it
greatly facilitates the development and implementation of new methods.
Nevertheless, I don't expect this (or any similar) library to become
"standard" soon; the approach is too new to be sure that a given design
will be good enough for the forseeable future.

> 4) Lets recall there is a language named CML that is currently 
> under development for WEB application. How does it fit the needs for 
> standards?

It attempts to provide standard data formats for certain applications,
which is definitely A Good Thing. I am not happy with CML in
particular, because it leaves many details open to interpretation. But
I do expect that XML-based file formats will help in creating standard
file formats.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------