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  • ...distance. The goal of this project is to implement support for phyloXML in BioRuby. [[BioRuby PhyloXML HowTo documentation]]
    16 KB (2,498 words) - 22:45, 7 November 2009
  • ...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) - 14:21, 14 August 2009
  • ...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) - 18:06, 22 September 2011
  • * 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) - 08:15, 3 July 2010

Page text matches

  • ...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) - 10:45, 5 September 2007
  • ...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) - 15:08, 8 November 2011
  • # '''Bioruby''': create object model for phylogenetic trees. Establish interface for exe
    2 KB (311 words) - 10:15, 26 September 2006
  • ...iojava.org BioJava], [http://biopython.org BioPython], [http://bioruby.org BioRuby], ...) have successfully provided a "glue" that allows interoperability of
    5 KB (605 words) - 16:20, 17 September 2013
  • ...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) - 16:44, 17 September 2013
  • ...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) - 15:23, 3 March 2008
  • ====BioRuby==== The BioRuby group contributed to this general use case by creating tools to read and wr
    6 KB (876 words) - 15:23, 3 March 2008
  • ====BioRuby==== The BioRuby group addressed this use case by adding functionality to calculate total tr
    7 KB (1,007 words) - 11:50, 5 September 2007
  • ===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) - 15:22, 3 March 2008
  • # ''BioRuby'' The BioRuby group developed a new NEXUS parser. The parser returns trees, data, charact
    41 KB (6,423 words) - 01:20, 30 March 2008
  • ...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) - 20:12, 22 October 2010
  • ...stitute || [mailto:czmasek%40burnham%2eorg czmasek@burnham.org] || Bioruby ...University of Tokyo || [mailto:k%40BioRuby%2eorg k@BioRuby.org] || Bioruby
    4 KB (528 words) - 17:43, 8 October 2008
  • ...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) - 10:03, 5 September 2007
  • ...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) - 10:04, 5 September 2007
  • ===BioRuby Targets===
    16 KB (2,329 words) - 10:27, 5 September 2007
  • ===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) - 20:11, 22 October 2010
  • ...]] 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) - 15:25, 23 December 2010
  • ...distance. The goal of this project is to implement support for phyloXML in BioRuby. [[BioRuby PhyloXML HowTo documentation]]
    16 KB (2,498 words) - 22:45, 7 November 2009
  • ...|| [[PhyloSoC:PhyloXML_support_in_BioRuby|Implementing phyloXML support in BioRuby]] || [[User:Czmasek|'''Chris Zmasek''']]; [[User:Pjotrp|Pjotr Prins]]
    2 KB (278 words) - 13:26, 12 March 2010
  • * [[PhyloSoC:PhyloXML_support_in_BioRuby|BioRuby implementation]] (current)
    1 KB (184 words) - 15:22, 23 December 2010
  • [[Category:Bioruby]]
    3 KB (492 words) - 14:42, 20 May 2009
  • ...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) - 14:21, 14 August 2009
  • '''Project:''' Implementing phyloXML support in BioRuby ...L] within the bioinformatics programming toolkit [http://www.bioruby.org/ BioRuby]. My code takes advantages of specialized XML libraries to boost the speed
    9 KB (1,344 words) - 21:01, 23 September 2009
  • ...0/nescent/t127230761223 Develop an API for NeXML I/O, and, RDF triples for BioRuby]</span> === ...XML I/O for BioRuby| Evolution and the semantic web in Ruby: NeXML I/O for BioRuby]] project idea.
    65 KB (9,936 words) - 15:24, 23 December 2010
  • ...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) - 18:04, 22 September 2011
  • === BioRuby forester === ...other computer programs or toolkits (such as [http://bioruby.open-bio.org/ BioRuby]). Although forester is mostly written in Java, it also contains components
    80 KB (12,076 words) - 06:01, 17 December 2012
  • ...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) - 18:06, 22 September 2011
  • * 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) - 08:15, 3 July 2010
  • '''Project:''' Develop an API for NeXML I/O, and, RDF triples for BioRuby ...ioRuby users to work seamlessly with NeXML files. My code integrates into BioRuby's existing framework for manipulating phylogenetic and comparative data on
    5 KB (753 words) - 17:06, 22 October 2010
  • ** BioRuby, Biopython, jsPhyloSVG, TreeGraph 2, TreeViewJ, TreeGradients, Treevolution
    2 KB (289 words) - 13:24, 1 June 2011
  • ...ing alignment classes and functions, or equivalents in BioPerl, BioJava or BioRuby (e.g.), will be helpful. Understanding of the practical uses of codon align
    65 KB (9,901 words) - 10:41, 14 February 2014