[Bioperl-l] Another implementation

J. H. Park jong@ebi.ac.uk
Wed, 13 Sep 2000 01:29:07 +0100


Thanks for your detailed picture. It is much clearer
to see :-) what your workbench and visual sequence
module is like.

> > Too much specifics to your DB will hurt your application's
> > future flexibility and standardization in my opinion.
> > A bit of thinking on that matter (interface between DB and parsers and
> > visualizations) will be good.
> > Cheers,
> >
> > Jong
> >
> Okay, thanx for all the input and interest.  We have been using the old
> David Searl's BioTk, with a few updates of our own mixed in.
> This is what we are thinking now:
> Given a valid BioPerl SeqI object,
> DrawableSequence (or Sequence::Drawable?) will create a zoomable,
> scrollable map with indices, labels, and different-coloured rectangles for
> each different kind of feature present.  It will be either vertical or
> horizontal depending on programmer preference.

> Workbench.pm will take a given SeqI and create two DrawableSequence
> objects: a DraftSeq and a FinishedSeq.  It will allow the user to select
> features from the DraftSeq, create genes comprising those features, and
> export them to the FinishedSeq.  The FinishedSeq will update itself with
> the new data and redraw itself.  Finished exons will be editable on a
> base-by-base level.

Sounds very useful(having 2 objects instead one).
> To make this all work, Workbench.pm will allow blast searches of clicked
> exons/groups of exons.  It will display translations of sequence, showing
> stop codons, etc.  It will display comments, etc. that are part of
> features that are clicked on in one of the DrawableSequences.
> In addition, our implementation of Workbench will examine blast results
> for each feature and be able to highlight all features that share
> homology.  This is available to us because of our db implementation, and
> because we have a dedicated linux beowulf cluster available for high-speed
> blast searches.

> We are actually close to delivering something like this.  Your input has
> helped reformat some of our objects, and hopefully this workbench can be
> usable no matter the data source.

It seems to me that your module will be the first proper perl
based visual workbench using objects. As a user's point of
view the design seems very good.

I just wonder if you can plug in gene prediction algorithm as
well as blast to any selected parts. This is because, sometimes,
people wonder some long and suspiscious introns are in fact
functional in some way. So, they may want to check the scores
of the original prediction(there are several simple and fast methods as I know).
(So, for this purpose, making some general plugging in gate will be good,
so that whenever people ask you can just call(plug in) available
algorithms and display the results).
I guess any such visual interface should be flexible in 
adding new algorithms underneath.

> Dave "Taking the chainsaw to DrawableSequence.pm now" Block

I hope to see your sawdusted result in the next bioperl conf. or any
journal in the future.



"It is easier to fight for principles than to live up to them."
-- Alfred Adler