| | 1 | = !BioRuby Topics = |
| | 2 | |
| | 3 | == Migration of BioRuby web resources == |
| | 4 | * rubyforge.org |
| | 5 | * gem (already available) |
| | 6 | * using BTS and Feature Requests in rubyforge.org ... Done |
| | 7 | * RDoc is moved to bioruby.rubyforge.org ... Done |
| | 8 | * Unused services should be disabled ... Done |
| | 9 | * open-bio.org |
| | 10 | * mailing list (already available) |
| | 11 | * preparation of MediaWiki by OBF server administrators ... Done |
| | 12 | * moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/ |
| | 13 | * migration from CVS to SVN |
| | 14 | * bioruby.org |
| | 15 | * moving wiki to bioruby.open-bio.org/Wiki |
| | 16 | * moving RDoc to bioruby.rubyforge.org ... Done |
| | 17 | * moving toppage to Wiki |
| | 18 | * tar.gz should move to ??? |
| | 19 | * www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?) |
| | 20 | |
| | 21 | == Bio::Sequence improvements for round trip == |
| | 22 | |
| | 23 | === Output (formatting) === |
| | 24 | * Bio::Sequence#output(format = ''anything'') |
| | 25 | * ERB templates |
| | 26 | * Bio::Sequence#output(format = :embl) |
| | 27 | * Bio::Sequence#output(format = :genbank) |
| | 28 | |
| | 29 | === Input (creation of Bio::Sequence object) === |
| | 30 | * Bio::Sequence#read(str or file?) or Bio::Sequence#input(str or file?) |
| | 31 | * Bio::*#to_biosequence is automatically called |
| | 32 | * Bio::*#to_biosequence |
| | 33 | |
| | 34 | === Easy access to Bio::Sequence inside BioRuby === |
| | 35 | * Bio::Sequence#embl, Bio::Sequence#gb |
| | 36 | * returns a wrapper object that acts as if it is Bio::EMBL or Bio::GenBank objects |
| | 37 | * delegates to Bio::Sequence objects (or translation/conversion may be needed) |
| | 38 | |
| | 39 | === Internal structure of Bio::Sequence === |
| | 40 | * generated from / compatible with XML Schema? |
