[BioPython] Creating a graphical interface to database of gene coordinates

[Leighton Pritchard]

Hi guys,

On Sat, 2006-04-22 at 13:32 +0100, Peter (BioPython) wrote:
> Srinivas Iyyer wrote:
> > Dear group, 
> >  I am happy that I am slowly finding pyhonian projects
> > related to my research area. 
> > 
> > Problem:
> > 1. I have a database of human gene coordinates on
> > chromosomes.
> > 2. I have gene expression data from my lab concerning
> > the genes I mentioned above. 
> > 
> > 3. I want to visualize expression data laid on
> > chromosomes.
> 
> You may be able to produce chromosome diagrams with Leighton Pritchard 
> and Jennifer White's program genomediagram:
> 
> http://bioinf.scri.sari.ac.uk/lp/programs.html#genomediagram
> 
> It will do both circular genomes diagrams (nice for bacteria) and linear 
> ones - which would make sense for chromosomes.  I think I've seen 
> examples with expression data shown in this way... certainly it could be 
> done.

We use it ourselves to plot array data against chromosome location, but
on the whole chromosome scale and, as you mention, not interactively.
It's pretty easy to do, but not what Srinivas is looking for, I think.
It sounds, Srinivas, like you're wanting something that will operate
more like GeneSpring?  Is that right?

It's possible that, if you just wanted to present a static image of
expression data, you could use GenomeDiagram in this way, but it's not
the way I would choose to present the data in a GUI - I'd expect drawing
straight onto a canvas (in whichever GUI toolkit suited you) to be more
flexible for you.

> Note that this can produce PDF or bitmap output - but its not 
> interactive.  There is also a GUI to go with it, but I have not looked 
> at this.

The GUI is pretty rudimentary, providing for file selection and just
enough document formatting so as to not be entirely useless to the non-
programmer.  An improved version (but still not interactive) is in a
perenially almost-ready state as wxPython widgets in the current source,
waiting for a serious fixing and a wxApp to hang from.

-- 
Dr Leighton Pritchard AMRSC
D131, Plant-Pathogen Interactions, Scottish Crop Research Institute
Invergowrie, Dundee, Scotland, DD2 5DA, UK
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