[Biojava-l] BioInformatics toolbox.

[Schreiber, Mark]

Yes you should know whats going on ...

However I am constantly frustrated by the number of biologists who don't
know how Blast works (or what an e score is) but take the results as
gospel :(

Anyhow, back to the topic. There is really know reason why algorithmic
proceedures can't be beaned especially if the right filters are in place
to take the output of one proceedure and plug it into the next. While
not algorithmic the biojava Blast/ HMMR parsing pipelines would be well
suited to the plug and play IDE design philosophy. It would make them a
hell of a lot more understandable to a novice programmer.

Mark

> -----Original Message-----
> From: Muratet, Michael [mailto:MMuratet@resgen.com] 
> Sent: Wednesday, 10 April 2002 3:51 a.m.
> To: 'Mario Gianota'; Michael L. Heuer
> Cc: biojava-l@biojava.org
> Subject: RE: [Biojava-l] BioInformatics toolbox.
> 
> 
> Greetings All
> 
> There is a tool like this for signal processing. Take a look 
> at Khoros at www-vis.lbl.gov. Its been a few years since I 
> used it, but the principle seems the same. The user can drag 
> and drop icons to form analysis chains that read, process, 
> and output data. Of course, you still have to know what's 
> going on inside a Fourier transform, just as a biologist 
> would have to know what's going on inside a gene finder (for 
> example) to make sense of the results. But you don't have to 
> code anything...
> 
> Regards,
> 
> Mike
> 
> 
> 
> > 
> > My idea is this: provide an IDE that is geared towards
> > developing visual
> > models of data sources. Parsers are associated with data 
> > sources and all
> > parsers can have data transformation filters attached to them which
> > implement a basic renderable interface so permiting the data to be
> > visualized. The IDE is plugin based in that additional 
> > parsers, renderers
> > and filters can be downloaded and plugged in. The filters 
> > offer a means to
> > transform the data through algorithmic means after it has 
> > been parsed and
> > before it hits any of the visualization components --so the 
> > entire process
> > from data aquisition to data transformation and visualization 
> > works on a
> > pipeline principle. This is a simple model which I believe 
> > that biologists
> > could get their heads around. The idea of 'pluggable' data 
> > transformation
> > algorithms shouldn't be too esoteric for them and it is a 
> > small step from
> > there towards getting the biologists to write their own 
> > plugins. This is why
> > I was looking at Eclipse.
> > 
> > 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================