[Biophp-dev] The humunguous IO class etc

Nico Stuurman biophp-dev@bioinformatics.org
Mon, 28 Apr 2003 12:01:28 -0700

> To me this does suggest a natural place to delineate between GenePHP
> and BioPHP - with GenePHP you appear to be moving towards almost a 
> pre-written
> application for handling gene and protein sequences, while I've been 
> focussed
> more on individual components that can be assembled in different ways 
> almost
> completely independent of each other (I have also been planning to go 
> beyond
> sequences at some point to include, e.g. phylogenetic trees 
> [indepedent of
> sequences, i.e. pre-calculated "newick" format trees], potentially HPLC
> Chromatograms and Mass Spectra, and so on).

> This suggests to me then that BioPHP serve as a "component 
> repository", while
> GenePHP remains the "implementation repository" where assembled 
> collections
> of components and components that are incorporated directly into the 
> GenePHP
> framework would go there.  Someone who wants to build a "custom"
> application or focussed "mini program" (i.e. for a public web page) 
> would
> do so with BioPHP components.  Someone looking for a "drop-in" 
> framework
> for a sequence-handling application would instead just use GenePHP.

> Does that make any sense?...

I thought that Serge hoped to develop a bioinformatics library, not an 
application.  Seems to be the same goal Sean had in mind with Biophp.  
I for one hope that the two of you can merge the projects sooner rather 
than later (also see my post concerning cvs), it would be a pity to 
dilute the efforts (and confuse outsiders) by splitting it in two.