[BioSQL-l] Plone4bio 1.0 and BioSQL

[Ivan Rossi]

On Thu, 1 Oct 2009, Peter wrote:

> Thanks for the report James!
>
> On Thu, Oct 1, 2009 at 2:20 PM, James Procter <jimp at compbio.dundee.ac.uk> wrote:
>>
>> * issue #2: The imagemap shown under the 'Features' tab is generated using
>> bioperl from a genbank file emitted by biopython. This is a flaw, and means
>> lots of info is lost (my biosql db is used to serve protein
>> sequence DAS annotation, so it has URLs, scores, and lots of notes).
>
> That is a curious and round about way of doing things, with many
> data transformations risking loosing things at each point.
>
> It would be possible to use Biopython's GenomeDiagram module to
> draw the image directly (although the style and capabilities would
> differ). I've done this for an in house TurboGears based BioSQL
> front end, and it was fine for prokaryotic organisms.

Hello Peter, happy that you are now on p4b too and not just many of us on 
biopython &;-)

We plan to remove the Bioperl-graphics option at some time, since we 
already need biopython for many things, and we are aware it is somewhat a 
kludge. Furthermore a full python implementation will be well-integrated 
within Zope HOWEVER there are valid technical reasons for that, the main 
one being that Bioperl-graphics is VERY advanced compared, in particular it 
automatically handles clashes of features lines and text, and map support. 
(click on a feature line to show a feature summary). They were not 
available at the time we evaluated GenomeDiagram (at the time it was not 
even in the standard distribution but just within Biopython CVS). And 
clashes-handling is a VERY DESIRABLE FEATURE if you always want readable 
images when you have lots of features of the same kind.

> Another more elegant alternative would be to call a BioPerl script which
> talks to the BioSQL database directly to get the data to draw the image.
>
> Can you point me at the relevant files in Plone4bio to see their code?
> I agree with your general point that a pluggable rendering option might
> be best, but that would be a question for the Plone4bio team to debate.

Pluggable rendering option will be GREAT. As I said above we think that 
having mixed-language code is a problem, and we would like a pure-python 
implementation.

Actually we started evaluation of genometools graphics too 
(see http://genometools.org/annotationsketch.html) since it has python 
bindings and looks nice, but other company priorities stalled it.
(read: we have to provide a working solution to a customer NOW)

We are open to contribution.

Ivan

--
Ivan Rossi, PhD - ivan AT biodec dot com
BioDec Srl, Via Calzavecchio 20/2, 40033 Casalecchio di Reno (BO), Italy
Phone: (+39)-051-0548263 - Fax: (+39)-051-7459582 - http://www.biodec.com