[Biojava-l] Re: [Bioperl-l] BioInformatics toolbox.

[Phillip Lord]

>>>>> "Robson" == Robson Francisco de Souza <rfsouza@citri.iq.usp.br> writes:

  >> If an open-source toolbox (gui based, not script) existed,
  >> perhaps those doing research could focus more of their efforts on
  >> research, rather than writing scripts around BioPerl, BioJava.

  Robson> 	By the way, implementing (really!) good alignment
  Robson> editors (e.g. BioEdit - unluckily Windows only!) and
  Robson> integrating the with search and retrieval routines to access
  Robson> Web databases and phylogenetic analysis programs would
  Robson> certainly be very, very nice!

There are certainly applications out there like this. JEmboss for
instance is a Java front end for the EMBOSS programs, running over
some sort of SOAP interface. It's uses Jalview internally as a
viewer. I've written a new version of Cinema, (sorry about the
terrible web page http://www.bioinf.man.ac.uk/dbbrowser/cinema-mx/),
which is heavily modular, and designed for just this sort of
thing. Unfortunately the actual code to interact with databases is
fairly immature, but it would serve as a starting point. And finally
ISYS is worth looking at as an integration suite, but sadly its not
free. 

This is all in Java. I have seen more in other languages, but I'm
afraid the URL's pass me by.


Phil