[Bioperl-l] Bio::Expression & Re: ReseqChip, module/package name

marian.thieme at arcor.de marian.thieme at arcor.de
Fri Aug 24 12:32:51 EDT 2007


> The new package: How about Bio::Expression::Tools::MitoChip?  My  
> reasoning: I don't think it's necessary to define a new  
> Bio::Resequencing namespace for just one module; my inclination is  
> towards using Bio::Expression namespace as Bio::Tools have been  
> traditionally reserved for output parsers.  I am unsure what the  
> Bio::Expression status is (very little is documented, no tests are  
> written, nothing on the mail list archives); maybe Allen can answer  
> that?  I don't see anything that precludes you from using that  
> namespace as long as your tools are fairly well-defined (they are)  
> and have tests (they do).

The problem I see, with Bio::Expression, is that Resequencing chips are not belongs to Expression chips.
(Expression chips are designed to hybridisize RNA strands and hence measure RNA expression levels, on the other hand a resequencing chip is based on DNA, also the design and the probe length is quite different). So, from my point of view it make sence to differ between dna and rna chips, at least.

> 
> Also, your module deals with doing one specific thing (extraction and  
> incorporation of information about redundant fragments) for the Affy  
> MitoChip.  It might be worth genericizing the class a bit so that you  
> can add new parser or analysis methods w/o having to define new  
> classes to deal with the same Mitochip data.

OK, need to think about that.

> 
> Mail list: The mail list subscription page (http://bioperl.org/ 
> mailman/listinfo/bioperl-l) allows you to subscribe or change  
> subscription options (at the bottom of the page).
> 
cleared

> Bugzilla: if you are logged into Bugzilla under your old email, there  
> is an option at the bottom of the page (Edit : Prefs) where you can  
> change your email address and other preferences.
> 
unfortunatly I dont recieve a mail to confirm the change. did try that twice..


Marian

> On Aug 24, 2007, at 5:05 AM, Marian Thieme wrote:
> 
> > Hi,
> >
> > 2 questions about the naming of the module I did submit
> > (see http://bugzilla.open-bio.org/show_bug.cgi?id=2332)
> >
> > 1.) The package:
> > because there exists already an expression package I suggest to  
> > create a
> > new package called resequencing
> >
> > 2.) I would suggest that the module is called RedundantFragments or
> > AdditionalFragments
> >
> > so we would have something like:
> >
> > Bio::Resequencing::AdditionalFragments
> >
> > Any other ideas ?
> >
> > Marian
> >
> > By the way can anybody change my email adress to  
> > marian.thieme at arcor.de
> > in bugzilla as well as in the bioperl list, please ?!! didnt achieve
> > that by my own...
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

Viel oder wenig? Schnell oder langsam? Unbegrenzt surfen + telefonieren
ohne Zeit- und Volumenbegrenzung? DAS TOP ANGEBOT FÜR ALLE NEUEINSTEIGER
Jetzt bei Arcor: günstig und schnell mit DSL - das All-Inclusive-Paket
für clevere Doppel-Sparer, nur  34,95 €  inkl. DSL- und ISDN-Grundgebühr!
http://www.arcor.de/rd/emf-dsl-2



More information about the Bioperl-l mailing list