= !BioRuby Topics = == Migration of BioRuby web resources == * rubyforge.org * gem (already available) * using BTS and Feature Requests in rubyforge.org ... Done * RDoc is moved to bioruby.rubyforge.org ... Done * Unused services should be disabled ... Done * open-bio.org * mailing list (already available) * preparation of MediaWiki by OBF server administrators ... Done * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/ ... in progress * (future work) migration from CVS to SVN * bioruby.org * moving wiki to bioruby.open-bio.org/Wiki * moving RDoc to bioruby.rubyforge.org ... Done * moving toppage to Wiki ... in progress * (future work) tar.gz should move to ??? * (future work) www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?) == !BioMoby client in Ruby == * ~~[wiki:MOBYRubyClient]~~ now working! == BioSQL on BioRuby == * rewritten by using !ActiveRecord == Bio::Sequence improvements for round trip == === Input (creation of Bio::Sequence object) === * Bio::Sequence#read(str ~~or file?~~~) ... Done * (or Bio::Sequence#input(str or file?) ???) * Bio::*#to_biosequence is automatically called ... Done * Bio::*#to_biosequence implementation * Bio::EMBL ... Done (jan) * Bio::GenBank ... Done (ngoto) === Output (formatting) === * Bio::Sequence#output(format = ''anything'') * using ERB templates * Bio::Sequence#output(format = :embl) ... in progress (jan) * Bio::Sequence#output(format = :genbank) ... in progress (ngoto) === Easy access to Bio::Sequence inside BioRuby === * (idea only) Bio::Sequence#embl, Bio::Sequence#gb * (idea only) can access as if it is Bio::EMBL or Bio::GenBank objects * (idea only) delegates to Bio::Sequence objects (or translation/conversion may be needed) * (idea only) Bio::EMBL (and GenBank etc.) changed to Bio::Sequence delegation objects? * jan's idea: BiorubyFormats * problem with lazy evaluation? === Internal structure of Bio::Sequence === * (future work?) generated from / compatible with XML Schema == NEXML parser in BioRuby == * (future work) generate parser code from XML schema == Which XML library is better in Ruby for BioRuby? == * REXML * xmlparser * ...