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.
Matthew 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:[EMAIL PROTECTED]] >>Sent: Wednesday, 10 April 2002 3:51 a.m. >>To: 'Mario Gianota'; Michael L. Heuer >>Cc: [EMAIL PROTECTED] >>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 - [EMAIL PROTECTED] >>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. > ======================================================================= > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
