I have been using BioX for things I want to publish but not take the time to fit into Bioperl.
I use NCBIx for anything strictly dependent on NCBI. Roger From: william.w...@gmail.com [mailto:william.w...@gmail.com] On Behalf Of Bill Ward Sent: Thursday, November 04, 2010 12:47 PM To: pignatelli_...@gva.es Cc: module-authors@perl.org Subject: Re: Naming a module: Non bioperl related Taxonomy modules I think if you put it under Bio:: then people will naturally assume that your modules are bioperl-related. Probably a different top level name is appropriate, maybe something starting with Bio. 2010/11/4 Miguel Pignatelli <pignatelli_...@gva.es> Dear all, I have written a small set of modules that have in common certain goals with the bioperl modules Bio::DB::Taxonomy(::flatfile) and Bio::Taxon. The main differences are: + No dependencies of non-standard Perl modules (VS tons of dependencies of bioperl modules) -- This is important in certain (and convenient) environments (like GRID or cloud systems) where you can't rely on automatic installation of big bundles. + NCBI and RDP taxonomies support (VS only NCBI support of bioperl modules) -- I plan to add support for additional taxonomies. + Very fast and low memory footprint (VS general poor performance of the bioperl bundle). Orders of magnitude even for the simplest lookups. + Fast mapping of different identifiers (VS lack of this feature in bioperl) Of course, these modules doesn't compete with Bio::DB::Taxonomy and Bio::Taxon in completeness of methods or integration with other tools (e.g. the rest of the bioperl bundle) but they are very handy (and actually being used by several bioinformatics groups) for fast mapping and large datasets analysis (frequent in bioinformatic analysis). The current (local) name of these modules are "Taxonomy", "Taxonomy::RDP", "Taxonomy::NCBI", "Taxonomy::NCBI::Gi2taxid" I have been told to put them in CPAN. Their natural location would be under the "Bio::" namespace. The bioperl developers don't have any problem with this as long as i) the documentation clearly states that these modules are not bioperl related and ii) the naming is sufficiently distinguishable from existing (bioperl) Taxonomy modules. Bioperl already have a Bio::Taxonomy::* (obsolete) and Bio::DB::Taxonomy::* which makes difficult the naming decision. I have in mind some alternatives like: Bio::Taxonomy::Lite::* Bio::DB::Taxonomy::Lite::* Bio::TaxDB::* Bio::TaxonomyDB::* Bio::TaxLite::* Bio::FastTaxonomy::* I don't know what is your feel about this. Any suggestion would be welcome. Best regards, M; -- Check out my LEGO blog at http://www.brickpile.com/ View my photos at http://flickr.com/photos/billward/ Follow me at http://twitter.com/williamward
