[Biojava-l] Gene Expression

[Gerald Loeffler]

hi!

my own project in that area deals mostly with cDNA-microarrays and their
production and usage. As such, it has the concepts of clone, clone
library, vector, plate, PCR, primer, array, array layout, spot, sample,
label, hybridisation, image analysis, spot values, and many more.

As i said, all of this is very much targeted at the production and usage
of cDNA-microarrays - but the resulting "expression values", which hide
in SpotValues objects, are there and are IMHO modelled nicely according
to the nature of the underlying process.

We could - if you want - try to design an object model for "expression
values" for which my types could serve as a starting point.

You should also have a look at the MGED working groups (hosted at EBI)
which target database "design", XML DTDs and other issues regarding
microarrays. These working groups were the result of (so far) 2 meetings
on microarray data standards. Especially the XML DTDs might be useful as
a starting point for Java types...

	cheers,
	gerald

Matthew Pocock wrote:
> 
> Jason Stajich wrote:
> 
> > I'm sure Matt will respond to this effect but check out
> > http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/
> >
> > Bioinformatics, Vol 16, no. 4 2000
> > Pages 402 - 403
> > [ if you have online access to the bioinformatics journal these should
> > work ]
> >
> > http://bioinformatics.oupjournals.org/cgi/content/abstract/16/4/402
> > http://bioinformatics.oupjournals.org/cgi/reprint/16/4/402
> >
> > -Jason
> >
> 
> Thanks for the plug Jason :-)
> 
> >
> > On Mon, 24 Jul 2000, Alex Tolley wrote:
> >
> > > Hi,
> > >    I am in the process of building some beans to analyse gene array
> > > expression data.  If you are going down that track as you imply, do you
> > > have any data structures for this in the pipline?  I would like my code
> > > to be inter-operable with yours where possible as I am getting very fed
> > > up reinventing the wheel.
> 
> The data-structures that I came up with were messy, hacky things that I
> ported from Perl. The visual display was nice though. The code for my
> expression browser is LGPLed, so feel free to pillage anything that looks
> usefull. Some of it should meander into BioJava as-and-when.
> 
> What data structures have you come up with so far? I know that there are
> others on the list with code and/or ideas for this already, so it would be
> realy good to get something hammered out.
> 
> An expression level is measured for a particular probe (spot on micro-array,
> primer pair in quantative PCR), and a particular condition (glucose level,
> temprature, delta-time...). A full experiment is a (possibly sparse) matrix
> of probe vs conditions. The expression level itself has a level and possibly
> lots of other stuff - optical intencity, evenness, error-margins. Many forms
> of measurement have images associated with sub-sets of the data - gell images
> for 1 primer pair over 12 conditions, or one didgitised micro-array.
> 
> Basicaly, some of these units will be usefull to everybody, so if anybody has
> a plan for what any of these look like, then please propose it.
> 
> Matthew
> 
> >
> > >
> > > Regards,
> > >
> > > --
> > > ==============================================
> > > Alex Tolley
> > > Snr. Software Engineer, Computational Sciences
> > > Iconix Pharmaceuticals
> > > 850 Maude Ave, Mountain View, CA 94043
> > >
> > > e-mail: atolley@iconixpharm.com
> > >
> > >
> > > _______________________________________________
> > > Biojava-l mailing list  -  Biojava-l@biojava.org
> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
> > Jason Stajich
> > jason@chg.mc.duke.edu
> > http://galton.mc.duke.edu/~jason/
> > (919)684-1806 (office)
> > (919)684-2275 (fax)
> > Center for Human Genetics - Duke University Medical Center
> > http://wwwchg.mc.duke.edu/
> >
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> 
> --
> Joon: You're out of your tree
> Sam:  It wasn't my tree
>                                                  (Benny & Joon)
> 
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-- 
   Gerald.Loeffler@vienna.at _________________ Software Architect
   http://www.imp.univie.ac.at ____ http://www.daemonstration.com
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