[Biojava-l] BioInformatics toolbox.

Matthew Pocock matthew_pocock@yahoo.co.uk
Fri, 12 Apr 2002 23:41:07 +0100

Hi Mark,

The org.biojava.bio.program.tagvalue package would also be very 
ameanable to graphical manipulation. Some of the classes would need 
beanifying (add no-arg constructors, and expose some fields as 
properties). Once that is done, you should be able to drag-and-drop file 
parsers together - imagine clicking a custom embl parser together 
visually, testing it on a few embl files, altering it visually, clicking 
on a bean and entering a bean shell statement as a custom call-back, 
running it again and then once working, connect it to a BioIndex object 
to build your customized EMBL indexes and cross-references, or feed it 
to the sequence gui package for display, or piping the results out as 
SQL statements. Makes me warm and tingley all over. I added some 
documentation to tagvalue today, so it may now make a bit more sence to 
the uninitiated.


Schreiber, Mark wrote:
> 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...
>>>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 
>>>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 
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