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  • PhyloSoC:PhyloXML support in BioRuby
    ...distance. The goal of this project is to implement support for phyloXML in BioRuby. [[BioRuby PhyloXML HowTo documentation]]
    16 KB (2,498 words) - 23:45, 7 November 2009
  • BioRuby PhyloXML HowTo documentation
    ...ng and exchanging data of annotated phylogenetic trees. PhyloXML parser in BioRuby is implemented in Bio::PhyloXML::Parser and writer in Bio::PhyloXML::Writer In addition to BioRuby library you need a libxml ruby bindings. To install:
    2 KB (358 words) - 15:21, 14 August 2009
  • NeXML and RDF API for BioRuby
    ...s page has moved to: https://github.com/rvosa/bio-nexml/wiki/NeXML-API-for-BioRuby [[Category:NeXML and RDF API for BioRuby]]
    152 bytes (22 words) - 19:06, 22 September 2011
  • Project Plan for NeXML and RDF API in BioRuby
    * Request for feedback from the BioRuby community( this will be done at the end of the week ) * Check out the serializer API in the [[NeXML and RDF API for BioRuby]].
    4 KB (696 words) - 09:15, 3 July 2010

Page text matches

  • Phylohackathon 1/First Call For Suggestions
    ...l is exclusionary to most other programmatic toolkits (BioJava, BioPython, BioRuby, etc.), it is only because of my unawareness of the phyloinformatic support
    11 KB (1,762 words) - 11:45, 5 September 2007
  • UseCases
    ...oke out into toolkit-specific groups (BioPerl, BioJava, BioSQL, BioPython, BioRuby) to carry out a gap analysis. Each group was tasked with identifying opport
    34 KB (4,831 words) - 16:08, 8 November 2011
  • WG:Participants
    # '''Bioruby''': create object model for phylogenetic trees. Establish interface for exe
    2 KB (311 words) - 11:15, 26 September 2006
  • Phylohackathon 1
    ...iojava.org BioJava], [http://biopython.org BioPython], [http://bioruby.org BioRuby], ...) have successfully provided a "glue" that allows interoperability of
    5 KB (605 words) - 17:20, 17 September 2013
  • Phylohackathon 1/Documentation
    ...r wrappers, such as code for PAUP and T_Coffee, are being developed by the BioRuby group. | created parser for BioRuby.
    6 KB (869 words) - 17:44, 17 September 2013
  • Family Alignment Documentation
    ...ioperl.org BioPerl], [http://biopython.org BioPython], [http://bioruby.org BioRuby]) since these packages offer the user different workflow possibilities and ===BioRuby===
    9 KB (1,461 words) - 16:23, 3 March 2008
  • Reconcile Trees Documentation
    ====BioRuby==== The BioRuby group contributed to this general use case by creating tools to read and wr
    6 KB (876 words) - 16:23, 3 March 2008
  • Phylogenetic Footprinting Documentation
    ====BioRuby==== The BioRuby group addressed this use case by adding functionality to calculate total tr
    7 KB (1,007 words) - 12:50, 5 September 2007
  • Morphological Characters Documentation
    ===BioRuby=== This use case has been addressed by developing a BioRuby NEXUS model and a NEXUS parser, as well as developing a parser for PAUP res
    4 KB (552 words) - 16:22, 3 March 2008
  • Supporting NEXUS
    # ''BioRuby'' The BioRuby group developed a new NEXUS parser. The parser returns trees, data, charact
    41 KB (6,423 words) - 02:20, 30 March 2008
  • Phyloinformatics Summer of Code 2007
    ...rg BioPerl], [http://www.biopython.org Biopython], [http://www.bioruby.org Bioruby], [http://www.swig.org SWIG], [https://sourceforge.net/projects/ncl NCL] ....org BioPerl]/[http://www.biopython.org Biopython]/[http://www.bioruby.org Bioruby]; [http://www.swig.org SWIG]; [http://dojotoolkit.org/ dojo]; [http://gride
    33 KB (4,999 words) - 21:12, 22 October 2010
  • Phylohackathon 1/Participants
    ...stitute || [mailto:czmasek%40burnham%2eorg czmasek@burnham.org] || Bioruby ...University of Tokyo || [mailto:k%40BioRuby%2eorg k@BioRuby.org] || Bioruby
    4 KB (528 words) - 18:43, 8 October 2008
  • Phylohackathon 1/Proposal
    ...rg Biojava], [http://www.biopython.org Biopython], [http://www.bioruby.org Bioruby], [http://www.blipkit.org Bioprolog]), which includes the most widely used # '''Bioruby''': create object model for phylogenetic trees (''there doesn't seem to be
    10 KB (1,452 words) - 11:03, 5 September 2007
  • Phylohackathon 1/Subgroup Proposals
    ...es and toolkits: Perl (Bioperl), Java (Biojava), Python (Biopython), Ruby (Bioruby), Prolog (Blipkit), R (Bioconductor?) ...es and toolkits: Perl (Bioperl), Java (Biojava), Python (Biopython), Ruby (Bioruby), Prolog (Blipkit), R (Bioconductor?)
    1 KB (201 words) - 11:04, 5 September 2007
  • Phylohackathon 1/Targets
    ===BioRuby Targets===
    16 KB (2,329 words) - 11:27, 5 September 2007
  • Phyloinformatics Summer of Code 2008
    ===phyloXML support in BioRuby=== .../en/ Ruby]. More specifically, extend the open source [http://bioruby.org/ BioRuby project] to support phyloXML. This will probably entail (i) the development
    56 KB (8,424 words) - 21:11, 22 October 2010
  • Phyloinformatics Summer of Code 2009
    ...]] project idea (namely, choosing Biopython as the Bio* library instead of BioRuby). ...how/google/gsoc2009/nescent/t124022800294 Implementing phyloXML support in BioRuby] ===
    78 KB (11,838 words) - 16:25, 23 December 2010
  • PhyloSoC:PhyloXML support in BioRuby
    ...distance. The goal of this project is to implement support for phyloXML in BioRuby. [[BioRuby PhyloXML HowTo documentation]]
    16 KB (2,498 words) - 23:45, 7 November 2009
  • Phyloinformatics Summer of Code 2009/Participants
    ...|| [[PhyloSoC:PhyloXML_support_in_BioRuby|Implementing phyloXML support in BioRuby]] || [[User:Czmasek|'''Chris Zmasek''']]; [[User:Pjotrp|Pjotr Prins]]
    2 KB (278 words) - 14:26, 12 March 2010
  • PhyloSoC:Biopython support for parsing and writing phyloXML
    * [[PhyloSoC:PhyloXML_support_in_BioRuby|BioRuby implementation]] (current)
    1 KB (184 words) - 16:22, 23 December 2010

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