Java or C++

Malay curiouser at ccmb.ap.nic.in
Wed Apr 12 14:14:11 EST 2000

Dear Nicolas:

> What a restricted view of the bioinformatics ...
I'd call pragmatic, realistic and deconstructive, that what modern biology

> Could I had all the modeling softwares, from the modelisation
> of structure (e.g. MODELLER) to the simulation of metabolic
> pathway. They do not deal with sequences, and they do not require
> visualisation as well.

Can you vouch for the non-requirement. Or just the absence of a facility
never made you realize what  you are missing. Can you deny a proper
visualization tool will greatly increase these programs' usability and

> Did you ever heard of GTK+ (http://www.gtk.org/)? This is a C
> library, not a C++. It is the library used by the GIMP and the
> GNOME project, which are not projects which "failed miserably".
> Try just to write one percent of gnumeric or GIMP and come back to
> presenty your results.

That's my point! Thanks for negeting your own argument. I can't write GIMP
in two years in C but can try writing it in C++ and Java. Not many programs
like GIMP are available and not on many systems. That's proves my point.
Softwares should be easily written and should be easily portable. If I can't
write a program that's means it's difficult to me, that in turn means that
the Gurus failed to deliver it to masses.

> Another exemple is Lesstif, the free replacement for motif toolkit
> see http://www.lesstif.org/

Yep! But not up to the mark!

> By the way, to answer your comment about Linux and the growing of
> C++ fashion, could I remind you that Linux is written in C?
> And more important XFREE IS WRITTEN IN C! (http://www.xfree86.org/)

Yep! But programs fro Linux will be written using C++. True for XFREE too
but how many program on Linux platform uses core API??

> Some link to visualisation softwares written in C:
> MOLMOL -> http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
> RASMOL -> http://www.bernstein-plus-sons.com/software/rasmol/
> GARLIC -> http://pref.etfos.hr/garlic

More and more written in C++ or Java
> But you have dosens of them. And you have dozens written in TCL,
> PERL or PYTHON linked with a toolkit.

Any how many users in day to day life uses them? These are softwares written
by programmers for the programmers.

> Please quit your Windows box five minutes and see the world before
> to claim manichean assertions.
That's the point. I pledge, beg and implore you, the bioinformatics guru
sitting in front of an 256MB SGI workstation that I work on a misly Windows
dumb box with only 32MB RAM  and all I have is shear intention to learn and
do something for all, windows, MAC, BeOS, OS/2 etc etc and to take me with
you along with my Windozzz box in this journey of new biology. And what  you
do? You advise to throw that box in gutter! World is chaning fast my friend.
All will be there, with all their bugs and assretion!

> Good luck for the future, and remember, diversity is fun and
> efficient, in computing as in biology,

Cut you own tail again! Just now you advised me to throw my box away.
Talking diversity.... Ah! At last! Diversity means not only the diversity of
language but also the diversity of OS. Along with language take the culture


Malay Kumar Basu
Centre for Cellular and Molecular Biology
Hyderabad 500007

Fax: (00-91)40-7171195
Phone: (00-91)40-7172241
Cataholic: Can't stop bringing cats home.
curiouser at ccmb.ap.nic.in


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