[Bioclusters] Java Vs C++(Qt) for Bioinformatics

Borries Demeler demeler at biochem.uthscsa.edu
Thu May 24 16:19:25 EDT 2007

Dear Aijaz,

Since I have not been using Java very much my input on this question will
be a bit biased. I have however used QT since version 2.3 to develop a
major, cross platform computational biology application that deals with
very large data sets and requires extensive 2D and 3D visualization.
QT has excellent support and is an excellent toolkit of extraordinarily
high quality. Also the documentation is superb. I can't say enough good
things about it and have never regretted deciding on it. Performance is
also great.

Qt also supports SQL and a large range of database engines, has sockets and
network primitives, a platform independent makefile system, threading,
internationalization, OpenGL support, a designer and XML support.

Good luck with your project, -Borries

> Hello All,
> Just wondering what bioinformatics community thinks of is best to use:
> 1. Java Swings (1.6+)
> 2. C++ Qt (4.0)
> My visualziation tool requires accessing data which is in the order of
> few hundred MBs we are expecting this to hit GBs soon. I am planning
> not to hold up all the data. However, I will have to hold up some data
> (a few hunderds of thousands (O(100,000)) of data entities, each costing
> around ~60 bytes). As the tool is supposed to be a interactive, what will
> be good alternative between Java Vs C++? I am leaning towards Java,
> reason being:
> 1. Comprehensive GUI
> 2. Java not that Slow, as they say!
> 3. Huge API, DBMS, XML, DRMAA, . . . . .
> 4. No deployment pain, although a little application
>    specific deployment may be required example: preference files etc
> 5. Automated Garbage collection, less trouble in maintaining memory.
>    Although it has a little overhead, it can be reduced by efficient
> handling of data???
> 6. efficient multi threading, not system level fork, etc??????
> 7. Java has growing number of Bioinformatics applications
> Kindly share your opinion regarding the aforementioned debate. Thank you for
> your
> time and participation!!
> Kind Regards,
> Aijaz.
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