[Biojava-l] Biobeans

[Ihab A.B. Awad]

Hi there,

According to "Wiepert, Mathieu" on Wednesday 26 September 2001 08:33:
> I ... found a link to biobeans (http://bioinf.gla.ac.uk/biobeans/), "an
> open-source project with the aim of providing biologists with a complete
> integrated data analysis environment".

Very interesting ... I was not aware of this, so thank you for the link!

I notice that the author is from the Comp Sci department at the University of 
Glasgow. There's been lots of really good research coming out of that dept, 
imho, and some of it has been related to bioinformatics.

They helped Sun build an orthogonally persistent Java platform, "PJama"; see 
the Glasgow site --

  http://www.dcs.gla.ac.uk/pjava/

and the SunLabs site --

  http://research.sun.com/forest/index.html

In the reports on PJama, they mention experiments using it to store a suffix 
tree for biological sequence similarity searching. I highly recommend the 
publications written about PJama, especially --

  http://research.sun.com/forest/COM.Sun.Labs.Forest.doc.pjama_review.abs.html

as well as the following paper, which was co-written by Malcolm Atkinson --

  Atkinson, M.A., and Morrison, R., Orthogonally Persistent Object
  Systems, The VLDB Journal 4, 3 (July 1995), 319-402.

  http://www.dcs.st-and.ac.uk/rsch/publications/AM95.shtml

The PJama project has been abandoned by Sun ... for reasons I can only guess 
at, and much to my personal disappointment, as I've been a fan of this 
technology for quite a while.

     *  *  *  *  *

One thing to mention is that, actually, I have been thinking of a 
NetBeans-like UI framework for bioniformatics; my contribution to the world 
in that vein is called FavaBeans --

  http://www.favabeans.org/

It is pretty generic at the moment -- no bio stuff yet -- but I'm in the 
process of trying to hook it up to some BioJava objects.

Regards & peace,

Ihab Awad

-- 
Ihab A.B. Awad <ihab@ahc.umn.edu>
Center for Computational Genomics and Bioinformatics,
University of Minnesota. http://www.cbc.umn.edu/~ihab/