[Bioperl-microarray] Re: [Biojava-l] News from BOSC

[Allen Day]

Mark, Everyone,

What we have in cvs right now is an IO system that works very similarly to
Bioperl's SeqIO.  It's set up to be able to handle IO subclasses that read
and write microarray file formats to/from an object model.  As I'm only
working with Affymetrix data (and the initiator of the bioperl microarray
effort), the only parsers in the cvs right now work on Affymetrix MAS 5.0,
Affymetrix CEL, and Affymetrix dChip tab delimited files.

Jim Lund at the Stanford Microarray Database is working on adding an
Affymetrix DAT (TIFF image) parser, so that we can extract out individual
spot images.  Gavin Sherlock at SMD also mentioned they plan to port their
GenePix and other array image file format parsers to the
bioperl-microarray object model, but I don't know what the progress is or
who's working on it.  Jim, can you comment on any of this?

As far as compatibility with other projects, I've tried to make the object
model somewhat resemble the relevant MAGE-OM modules.  At some point it
would be nice to have bridges between Bio::MAGE and bioperl-microarray,
but it hasn't been done yet (ie, I haven't had a need to export MAGE-ML
yet).  No other compatibilities have been considered, are there efforts I
should be aware of?

-Allen




On Sun, 29 Jun 2003, Jason Stajich wrote:

> we've started some things over on the bioperl side - but I'm not clear how
> much of the object model is reusable.  perhaps as you start to write
> things you can sketch some obj diagrams?
> 
> -j
> 
> On Mon, 30 Jun 2003, Schreiber, Mark wrote:
> 
> > Hi All,
> >
> > Bosc in brisbane was very cool (as usual). Interesting to note a large number of people wanting micro-array support in the bio* packages.
> >
> > I had a chat with Brad Chapman and he is cool with us porting some of the micro array stuff biopython has. I figure it make sense for the bio* people to keep a fairly uniform object model. This is the reason why bioSQL works and should be useful if the bio*s ever need to make a micro array exchange point like bioSQL.
> >
> > Just my thoughts,
> >
> > - mark
> >
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> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>