[BioSQL-l] [P4b] Plone4bio 1.0 and BioSQL

[Peter]

On Thu, Oct 1, 2009 at 4:22 PM, Ivan Rossi <ivan at biodec.com> wrote:
>
> Hello Peter, happy that you are now on p4b too and not just many of us on
> biopython &;-)

Hi!

Looking at the Plone4bio.org website I was surprised to see no mention
of BioSQL, Biopython on the install page (while BioPerl is mentioned):
http://plone4bio.org/trac/wiki/Install

I did eventually find the Manifesto page, but think it could be a little
more prominent (or even merged into the main page?)
http://plone4bio.org/trac/wiki/Manifesto

>From the way you are using Biopython for GenBank output, I guess
you need at least Biopython 1.51 for the feature support, but other
than that I am not clear how extensively Biopython is used.

P.S. The Manifesto page has a broken link to Plone (first paragraph),
and officially it should be Biopython not 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.

For now, GenomeDiagram requires you to put features on different
tracks explicitly to avoid overlaps or clashes. Not ideal for your needs.

What did you mean by "map support"? ReportLab's trunk (i.e. pre 2.4)
has good SVG output, and I have been meaning to contribute basic
HTML image map output to them. Either of these can be used with
Biopython's GenomeDiagram and a tiny patch to make diagrams with
click-able features. This worked pretty well I found.

Peter