April 2007 Archives by subject

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Starting: Mon Apr 2 12:55:28 UTC 2007
Ending: Mon Apr 23 20:05:36 UTC 2007
Messages: 113

• [BioRuby-cvs] bioruby ChangeLog,1.62,1.63   Naohisa Goto
• [BioRuby-cvs] bioruby COPYING, 1.1.1.1, NONE COPYING.LIB, 1.1.1.1, NONE   Katayama Toshiaki
• [BioRuby-cvs] bioruby README,1.14,1.15 README.DEV,1.12,1.13   Katayama Toshiaki
• [BioRuby-cvs] bioruby README,1.15,1.16   Trevor Wennblom
• [BioRuby-cvs] bioruby README.DEV,1.13,1.14   Trevor Wennblom
• [BioRuby-cvs] bioruby/bin bioruby, 1.18, 1.19 br_biofetch.rb, 1.3, 1.4 br_bioflat.rb, 1.16, 1.17 br_biogetseq.rb, 1.3, 1.4 br_pmfetch.rb, 1.6, 1.7   Trevor Wennblom
• [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.18,1.19   Naohisa Goto
• [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.19,1.20   Naohisa Goto
• [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.20,1.21   Naohisa Goto
• [BioRuby-cvs] bioruby/lib bio.rb,1.82,1.83   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib bio.rb,1.83,1.84   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio alignment.rb, 1.21, 1.22 command.rb, 1.16, 1.17 db.rb, 0.36, 0.37 feature.rb, 1.12, 1.13 location.rb, 0.27, 0.28 pathway.rb, 1.35, 1.36 reference.rb, 1.23, 1.24 sequence.rb, 0.57, 0.58 tree.rb, 1.7, 1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio map.rb,1.10,1.11   Jan Aerts
• [BioRuby-cvs] bioruby/lib/bio map.rb,1.9,1.10 shell.rb,1.18,1.19   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl blast.rb, 1.32, 1.33 clustalw.rb, 1.17, 1.18 emboss.rb, 1.7, 1.8 fasta.rb, 1.23, 1.24 hmmer.rb, 1.8, 1.9 mafft.rb, 1.16, 1.17 psort.rb, 1.12, 1.13 pts1.rb, 1.4, 1.5 sim4.rb, 1.9, 1.10   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl mafft.rb,1.15,1.16   Naohisa Goto
• [BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.7,1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.19, 1.20 format8.rb, 1.6, 1.7 report.rb, 1.10, 1.11 rexml.rb, 1.11, 1.12 wublast.rb, 1.8, 1.9 xmlparser.rb, 1.16, 1.17   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.20, 1.21 wublast.rb, 1.9, 1.10   Naohisa Goto
• [BioRuby-cvs] bioruby/lib/bio/appl/blast format0.rb, 1.21, 1.22 wublast.rb, 1.10, 1.11   Naohisa Goto
• [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.12,1.13   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.11,1.12   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/fasta format10.rb,1.6,1.7   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/appl/fasta format6.rb,1.2,NONE   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/appl/gcg msf.rb, 1.1, 1.2 seq.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.9,1.10   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/hmmer report.rb,1.12,1.13   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/iprscan report.rb,1.5,1.6   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.11,1.12   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/phylip alignment.rb, 1.1, 1.2 distance_matrix.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/psort report.rb,1.14,1.15   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/sim4 report.rb,1.8,1.9   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/sosui report.rb,1.10,1.11   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/spidey report.rb,1.9,1.10   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/targetp report.rb,1.8,1.9   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/appl/tmhmm report.rb,1.7,1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/data aa.rb, 0.19, 0.20 codontable.rb, 0.17, 0.18 na.rb, 0.21, 0.22   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/data aa.rb, 0.20, 0.21 na.rb, 0.22, 0.23   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/data aa.rb,0.21,0.22   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/data na.rb,0.20,0.21   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db aaindex.rb, 1.19, 1.20 fantom.rb, 1.13, 1.14 fasta.rb, 1.27, 1.28 gff.rb, 1.7, 1.8 go.rb, 1.10, 1.11 lasergene.rb, 1.2, 1.3 litdb.rb, 0.9, 0.10 medline.rb, 1.15, 1.16 nbrf.rb, 1.9, 1.10 newick.rb, 1.6, 1.7 nexus.rb, 1.2, 1.3 pdb.rb, 1.7, 1.8 rebase.rb, 1.7, 1.8 soft.rb, 1.1, 1.2 transfac.rb, 1.11, 1.12   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db/embl common.rb, 1.11, 1.12 embl.rb, 1.28, 1.29 sptr.rb, 1.35, 1.36 swissprot.rb, 1.6, 1.7 trembl.rb, 1.6, 1.7 uniprot.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb, 1.10, 1.11 ddbj.rb, 1.8, 1.9 genbank.rb, 0.39, 0.40 genpept.rb, 1.11, 1.12 refseq.rb, 1.7, 1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db/kegg brite.rb, 0.7, 0.8 compound.rb, 0.14, 0.15 drug.rb, 1.1, 1.2 enzyme.rb, 0.10, 0.11 expression.rb, 1.10, 1.11 genes.rb, 0.24, 0.25 genome.rb, 0.16, 0.17 glycan.rb, 1.4, 1.5 keggtab.rb, 1.9, 1.10 kgml.rb, 1.6, 1.7 reaction.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db/kegg ortholog.rb,1.7,1.8   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/db/kegg orthology.rb,1.8,1.9   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.7, 1.8 chain.rb, 1.7, 1.8 chemicalcomponent.rb, 1.2, 1.3 model.rb, 1.8, 1.9 pdb.rb, 1.20, 1.21 residue.rb, 1.11, 1.12 utils.rb, 1.6, 1.7   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.21,1.22   Naohisa Goto
• [BioRuby-cvs] bioruby/lib/bio/db/pdb residue.rb,1.12,1.13   Naohisa Goto
• [BioRuby-cvs] bioruby/lib/bio/io das.rb, 1.15, 1.16 dbget.rb, 1.12, 1.13 ddbjxml.rb, 1.13, 1.14 ebisoap.rb, 1.2, 1.3 ensembl.rb, 1.10, 1.11 fastacmd.rb, 1.15, 1.16 fetch.rb, 1.9, 1.10 flatfile.rb, 1.57, 1.58 keggapi.rb, 1.13, 1.14 ncbisoap.rb, 1.2, 1.3 pubmed.rb, 1.15, 1.16 registry.rb, 1.18, 1.19 soapwsdl.rb, 1.6, 1.7 sql.rb, 1.7, 1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/io flatfile.rb,1.58,1.59   Katayama Toshiaki
• [BioRuby-cvs] bioruby/lib/bio/io/flatfile bdb.rb, 1.9, 1.10 index.rb, 1.18, 1.19 indexer.rb, 1.24, 1.25   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/sequence aa.rb, 1.3, 1.4 common.rb, 1.3, 1.4 compat.rb, 1.3, 1.4 format.rb, 1.3, 1.4 generic.rb, 1.4, 1.5 na.rb, 1.5, 1.6   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/sequence na.rb,1.6,1.7   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/shell core.rb, 1.23, 1.24 demo.rb, 1.3, 1.4 interface.rb, 1.15, 1.16 irb.rb, 1.2, 1.3 object.rb, 1.2, 1.3 script.rb, 1.2, 1.3 setup.rb, 1.2, 1.3 web.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/shell/plugin blast.rb, 1.2, 1.3 codon.rb, 1.15, 1.16 das.rb, 1.2, 1.3 emboss.rb, 1.2, 1.3 entry.rb, 1.9, 1.10 keggapi.rb, 1.11, 1.12 midi.rb, 1.8, 1.9 psort.rb, 1.2, 1.3 seq.rb, 1.20, 1.21   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/shell/plugin flatfile.rb, 1.12, 1.13 obda.rb, 1.9, 1.10   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util color_scheme.rb, 1.3, 1.4 contingency_table.rb, 1.6, 1.7 restriction_enzyme.rb, 1.12, 1.13 sirna.rb, 1.10, 1.11   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/color_scheme buried.rb, 1.3, 1.4 helix.rb, 1.3, 1.4 hydropathy.rb, 1.3, 1.4 nucleotide.rb, 1.3, 1.4 strand.rb, 1.4, 1.5 taylor.rb, 1.3, 1.4 turn.rb, 1.3, 1.4 zappo.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.10, 1.11   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.12, 1.13   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis_basic.rb, 1.13, 1.14   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme single_strand.rb, 1.4, 1.5 integer.rb, 1.2, NONE   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.15, 1.16 analysis_basic.rb, 1.9, 1.10 double_stranded.rb, 1.8, 1.9 single_strand.rb, 1.3, 1.4 single_strand_complement.rb, 1.2, 1.3 string_formatting.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.16, 1.17 analysis_basic.rb, 1.11, 1.12 cut_symbol.rb, 1.4, 1.5 double_stranded.rb, 1.9, 1.10 single_strand.rb, 1.5, 1.6 single_strand_complement.rb, 1.3, 1.4 string_formatting.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme analysis.rb, 1.17, 1.18   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme enzymes.yaml, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/double_stranded aligned_strands.rb, 1.3, 1.4 cut_location_pair.rb, 1.5, 1.6 cut_location_pair_in_enzyme_notation.rb, 1.3, 1.4 cut_locations.rb, 1.3, 1.4 cut_locations_in_enzyme_notation.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/double_stranded aligned_strands.rb, 1.4, 1.5 cut_location_pair.rb, 1.7, 1.8 cut_location_pair_in_enzyme_notation.rb, 1.5, 1.6 cut_locations.rb, 1.4, 1.5 cut_locations_in_enzyme_notation.rb, 1.5, 1.6   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/double_stranded cut_location_pair.rb, 1.6, 1.7 cut_location_pair_in_enzyme_notation.rb, 1.4, 1.5 cut_locations_in_enzyme_notation.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range cut_range.rb, 1.1, 1.2 cut_ranges.rb, 1.2, 1.3 horizontal_cut_range.rb, 1.2, 1.3 sequence_range.rb, 1.5, 1.6 vertical_cut_range.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range cut_range.rb, 1.2, 1.3 cut_ranges.rb, 1.3, 1.4 horizontal_cut_range.rb, 1.3, 1.4 sequence_range.rb, 1.6, 1.7 vertical_cut_range.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range/sequence_range calculated_cuts.rb, 1.4, 1.5 fragment.rb, 1.2, 1.3 fragments.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range/sequence_range calculated_cuts.rb, 1.5, 1.6 fragment.rb, 1.3, 1.4 fragments.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand cut_locations_in_enzyme_notation.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand cut_locations_in_enzyme_notation.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/single_strand cut_locations_in_enzyme_notation.rb, 1.5, 1.6   Trevor Wennblom
• [BioRuby-cvs] bioruby/sample color_scheme_na.rb, 1.2, 1.3 goslim.rb, 1.4, 1.5 psortplot_html.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/sample color_scheme_na.rb,1.1,1.2   Mitsuteru C. Nakao
• [BioRuby-cvs] bioruby/sample goslim.rb,1.3,1.4   Mitsuteru C. Nakao
• [BioRuby-cvs] bioruby/sample psortplot_html.rb,1.1,1.2   Mitsuteru C. Nakao
• [BioRuby-cvs] bioruby/test/functional/bio/io test_ensembl.rb, 1.3, 1.4 test_soapwsdl.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb, 1.10, 1.11 test_command.rb, 1.4, 1.5 test_db.rb, 1.3, 1.4 test_feature.rb, 1.4, 1.5 test_location.rb, 1.3, 1.4 test_map.rb, 1.4, 1.5 test_pathway.rb, 1.4, 1.5 test_reference.rb, 1.2, 1.3 test_sequence.rb, 1.8, 1.9 test_shell.rb, 1.6, 1.7 test_tree.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb, 1.9, 1.10 test_feature.rb, 1.3, 1.4 test_location.rb, 1.2, 1.3 test_pathway.rb, 1.3, 1.4 test_sequence.rb, 1.6, 1.7   Mitsuteru C. Nakao
• [BioRuby-cvs] bioruby/test/unit/bio test_map.rb,1.5,1.6   Jan Aerts
• [BioRuby-cvs] bioruby/test/unit/bio test_sequence.rb,1.7,1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl test_blast.rb, 1.4, 1.5 test_fasta.rb, 1.2, 1.3 test_pts1.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/bl2seq test_report.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/blast test_report.rb, 1.4, 1.5 test_xmlparser.rb, 1.6, 1.7   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/genscan test_report.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/hmmer test_report.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/sosui test_report.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/targetp test_report.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/appl/tmhmm test_report.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/data test_aa.rb, 1.5, 1.6 test_codontable.rb, 1.5, 1.6 test_na.rb, 1.8, 1.9   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/data test_aa.rb,1.6,1.7   Katayama Toshiaki
• [BioRuby-cvs] bioruby/test/unit/bio/data test_na.rb,1.7,1.8   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/db test_aaindex.rb, 1.3, 1.4 test_fasta.rb, 1.4, 1.5 test_gff.rb, 1.5, 1.6 test_lasergene.rb, 1.1, 1.2 test_newick.rb, 1.4, 1.5 test_nexus.rb, 1.1, 1.2 test_prosite.rb, 1.5, 1.6 test_rebase.rb, 1.4, 1.5 test_soft.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_common.rb, 1.3, 1.4 test_embl.rb, 1.4, 1.5 test_embl_rel89.rb, 1.1, 1.2 test_sptr.rb, 1.6, 1.7 test_uniprot.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/db/kegg test_genes.rb,1.4,1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/db/pdb test_pdb.rb,1.2,1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/io test_ddbjxml.rb, 1.3, 1.4 test_ensembl.rb, 1.5, 1.6 test_fastacmd.rb, 1.2, 1.3 test_flatfile.rb, 1.1, 1.2 test_soapwsdl.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/sequence test_aa.rb, 1.2, 1.3 test_common.rb, 1.3, 1.4 test_compat.rb, 1.2, 1.3 test_na.rb, 1.4, 1.5   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/sequence test_aa.rb,1.3,1.4   Katayama Toshiaki
• [BioRuby-cvs] bioruby/test/unit/bio/sequence test_na.rb,1.3,1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/shell/plugin test_seq.rb, 1.8, 1.9   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util test_color_scheme.rb, 1.2, 1.3 test_contingency_table.rb, 1.3, 1.4 test_restriction_enzyme.rb, 1.2, 1.3 test_sirna.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.10, 1.11   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_analysis.rb, 1.9, 1.10 test_cut_symbol.rb, 1.1, 1.2 test_double_stranded.rb, 1.4, 1.5 test_single_strand.rb, 1.2, 1.3 test_single_strand_complement.rb, 1.2, 1.3 test_string_formatting.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme test_integer.rb, 1.2, NONE   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme/analysis test_calculated_cuts.rb, 1.3, 1.4 test_cut_ranges.rb, 1.1, 1.2 test_sequence_range.rb, 1.3, 1.4   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme/double_stranded test_aligned_strands.rb, 1.2, 1.3 test_cut_location_pair.rb, 1.2, 1.3 test_cut_location_pair_in_enzyme_notation.rb, 1.2, 1.3 test_cut_locations.rb, 1.2, 1.3 test_cut_locations_in_enzyme_notation.rb, 1.2, 1.3   Trevor Wennblom
• [BioRuby-cvs] bioruby/test/unit/bio/util/restriction_enzyme/single_strand test_cut_locations_in_enzyme_notation.rb, 1.2, 1.3   Trevor Wennblom

Last message date: Mon Apr 23 20:05:36 UTC 2007
Archived on: Mon Jun 16 03:01:38 UTC 2014

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