Comments on Java applet development for biosciences

Luca Ida Giovanni TOLDO (Ph.D.) toldo at embl-heidelberg.de
Tue Apr 30 15:45:09 EST 1996

I recently read this posting about Java and Molecular Biology,
and due to my activities in this context ( development of a
Java-based Molecular Biology workbench / tivoli: see
http://www.embl-heidelberg.de/~toldo/JaMBW.html) and also of
a meeting on the topic held on the 29 April and announced in
bionet.software as well...

It is a very interesting mail.

Don Gilbert wrote:
>    1) how easy is Java to learn and use?
> I had little problem with Java in part because I've been writing
> complex GUI-based programs in C++ for a few years now.  Java is
> close enough to C++ that someone who knows one can do the other
> (though I'd recommend for a student to learn C++ first, as Java
> seems to be a somewhat odd subset of C++).

I do not agree with the bracketed comment. Infact, "Java is C++--"
(quoted from an active Bio-OO developer named Georg Tuparev).
Beyond the "academic" debate on C++ versus Java, I just would like
to make the point that no C++ knowledge is required for programming
in Java. It is required, anyhow, to have some understanding of OO
and / or at least being OO-compliant. For the whole remaining part
of the text, I agree fully with the variant that I learned Java
also using some books (Java in a Nutshell and Essential Java).

>    2) How is the Java Applet being developed, by professional 
>software engineers, scientists both?
100 % fine.
>   3) Approximately how long did the app take to design to the current point?
100 % identical, with the variant that having done the development
on Macintosh I had 0 time to spend on that topic since everything run
perfect (specially on the 7200 and higher) using the JDK. (do not waste
time with Caffeine ... that was the only one I really wasted)
> 4) What do you think the advantages are to users and designers of 
>this type of approach?

down to this point I agree but the next ones ..

> These new methods will offer some advantages, but not necessarily outstanding
> advantages compared to older programming technologies like Hypercard,
> Visual Basic and languages like SmallTalk & C++.  In large measure we will
> have to wait to see what the advantages are.

I do not think that we have to wait ... the advantages are clear there,
is just the creativity that is missing. 

> But in the near term, I find Java
> a compelling method to provide flexible Internet client programs that
> I don't find in any other current development system.

Not only for Internet client programs but for anything else as well !
With the premise, of course, of not try to rewrite Word in Java...

>     Are there any other comments you'd like to make on scientific apps. and
>    the WWW?
> At this point (April 96) it is pretty early in Java use for me to recommend
> it for the average scientist to develop or to use.  Java is still buggy as a development system.  Development software for it is still
> in an early stage.  Display software is buggy and limited
> (Netscape, Appletviewer).   If you work with it now, you will have
> to battle bugs in the development and display software as well as
> problems of your own making.

I do not agree fully, but partially. As is now it is pretty buggy,
but at each new version of the various readers available (Netscape
Atlas PR2 is really great, Internet Explorer 3.0 promises Java 
capabilities, HotJava, APpletViewer) things gets better ...

In other words: start coding in java now if you want to be "good
enough" when it will be "established" ...

looking forward your comments (also on my JaMBW project ...)


Dr. Luca Ida Giovanni TOLDO (Ph.D.)
European Molecular Biology Laboratory
Computer Group

p.s. minutes of the JaMBW meeting will appear soon ... together
with my the JAVA-crash-course for bio-applets which I distributed
at the meeting ...

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