[Biopython-dev] Active projects list? (BOSC Biopython Project Update)

[Tiago Antão]

On Sat, Jul 3, 2010 at 7:52 AM, Andrea Pierleoni
<andrea at biocomp.unibo.it> wrote:
> 1) together with Mauro Amico, we hare developing a graphical library very
> similar to the Bio::Graphics module pf BioPerl. The project is at good
> point, and will come with documentation and tutorial as a standalone
> package we call BioGraPy. I know that in biopython one can already use
> GenomeDiagram to draw, for example, seqrecord features, but this could
> extend biopython plotting capability significantly. You can use BioGraPy
> to plot a blast output (with its HTML map), to plot hydrophobicity plot
> along the sequence (read as per letter annotations), mRNA and CDS with
> their splicing sites, and so on... BioGrapy relies on matplotlib, so this
> will be an additional external dependence, but worthwhile in my opinion.

2 comments:

1. Strong support for matplotlib dependence. As usual it is very easy
to shield the code against forcing people to install matplotlib (this
is not a C library type of dependency where things would be more
serious). The dependency is only needed for people who want to use
your code. So this is not a big problem. matplotlib is also very
standard in scientific python, not a marginal application. Thumbs up,
IMHO. matplotlib, numpy and scipy are no brainers in my opinion.
2. The bioperl name bio::graphics strikes me as not completely
perfect. I say this because there is more to bioinformatics than
sequence analysis. Whatever naming convention is assumed in biopython
for any kind of graphics, there should be some care with this. ;) .
That being said, I think it is great that charting support exists.

My .02 € (loosing value by the day),
Tiago