From allenday at ucla.edu Sun Jun 8 16:25:40 2003 From: allenday at ucla.edu (Allen Day) Date: Sun Jun 8 18:25:57 2003 Subject: [bioperl-microarray] test Message-ID: From crsto at ucla.edu Mon Jun 16 18:31:57 2003 From: crsto at ucla.edu (Chris To) Date: Mon Jun 16 21:32:49 2003 Subject: [Bioperl-microarray] Changes to parser modules Message-ID: <200306170131.h5H1VvH29095@webmail.my.ucla.edu> This is a list of the significant "naming changes" recently made to the bioperl-microarray parser modules In order to follow MAGE naming conventions and also clean up/clarify some of the Bioperl-Microarray modules, the following changes were made: Modules are now all documented! Changes to Bio::Expression::Microarray::MicroarrayIO ---------------------------------------------------- Module naming (affymetrix.pm, dchipxls.pm mas50txt.pm) and their interfaces remain the same. However the internals have been modified to reflect changes in the Affy Array module changes that are detailed below. Changes to Bio::Expression::Microarray::Affymetrix:: modules ------------------------------------------------------------ Array.pm renamed to ArrayDesign.pm Data.pm renamed to CelArray.pm Feature.pm unchanged Mas50Data.pm renamed Mas50TxtArray.pm dChipXLS.pm renamed dChipArray.pm IN ALL above modules where appropriate: Method Changes featureset renamed featuregroup each_featureset renamed each_featuregroup qc_featureset renamed qc_featuregroup each_qcfeaturegroup renamed each_qcfeaturegroup Send any comments or questions to allenday@ucla.edu and crsto@ucla.edu. From allenday at ucla.edu Sun Jun 29 20:18:10 2003 From: allenday at ucla.edu (Allen Day) Date: Sun Jun 29 22:17:56 2003 Subject: [Bioperl-microarray] Re: [Biojava-l] News from BOSC In-Reply-To: Message-ID: 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 > > > > ======================================================================= > > Attention: The information contained in this message and/or attachments > > from AgResearch Limited is intended only for the persons or entities > > to which it is addressed and may contain confidential and/or privileged > > material. Any review, retransmission, dissemination or other use of, or > > taking of any action in reliance upon, this information by persons or > > entities other than the intended recipients is prohibited by AgResearch > > Limited. If you have received this message in error, please notify the > > sender immediately. > > ======================================================================= > > > > _______________________________________________ > > Biojava-l mailing list - Biojava-l@biojava.org > > http://biojava.org/mailman/listinfo/biojava-l > > > > -- > Jason Stajich > Duke University > jason at cgt.mc.duke.edu >