Paul Sculfor Bio

Bio::Ontology::Ontology is a standard implementation of an Ontology. SYNOPSIS use Bio::Ontology::Ontology; # create ontology object my $ont = Bio::Ontology::Ontology->new(-name => "OBF"); # add terms, relationships ... my $bp = Bio::Ontology::Term->new(-name => "Bioperl"); my $obf =... Platforms: *nix

Bio::MAGE::Protocol::SoftwareApplication is a Perl module. SYNOPSIS use Bio::MAGE::Protocol::SoftwareApplication; # creating an empty instance my $softwareapplication = Bio::MAGE::Protocol::SoftwareApplication->new(); # creating an already populated instance my $softwareapplication =... Platforms: *nix

Bio::DB::GFF::Feature is a relative segment identified by a feature type. Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and... Platforms: *nix

bio2jack is a library that allows for simple porting of general purposed bio (blocked io) OSS/ALSA audio applications to Jack. This library allows the person porting the code to simply replace the calls into OSS/ALSA with calls into interface functions of this library. The library buffers a... Platforms: *nix

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file. SYNOPSIS if ( $type =~ /trees/i ) { $block_object = new Bio::NEXUS::TreesBlock( $block_type, $block, $verbose ); } If a NEXUS block is a Trees Block, this module parses the block and stores the tree data.... Platforms: *nix

Bio::TreeIO::svggraph is a simple output format that converts a Tree object to an SVG output. SYNOPSIS use Bio::TreeIO; my $in = new Bio::TreeIO(-file => input, -format => newick); my $out = new Bio::TreeIO(-file => >output, -format => svggraph); while( my $tree = $in->next_tree ) { my... Platforms: *nix

Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file. SYNOPSIS if ( $type =~ /unaligned/i ) { $block_object = new Bio::NEXUS::UnalignedBlock($type, $block, $verbose); } This is a class representing an unaligned block in NEXUS file METHODS new... Platforms: *nix

Bio::NEXUS::Functions is a Perl module that provides private utility functions for the module. This package provides private functions that are not object-specific.. Platforms: *nix

Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). SYNOPSIS new Bio::NEXUS::WeightSet($name, @weights, $iswt); A module representing column weights in alignment (for each character) METHODS new Title : new Usage : $node = new... Platforms: *nix

Bio::Location::CoordinatePolicyI is an abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location. SYNOPSIS # get a location, e.g., from a SeqFeature $location = $feature->location(); # examine its coordinate computation policy print... Platforms: *nix

Bio::Phylo::Treedrawer::Svg is a Perl module that creates svg tree drawings. No serviceable parts inside. This module creates a scalable vector graphic from a Bio::Phylo::Trees::Tree object. It is called by the Bio::Phylo::Treedrawer object, so look there to learn how to create tree drawings.... Platforms: *nix

Bio::NEXUS::NotesBlock is a Perl module that represents a NOTES block in a NEXUS file. Placeholding module for the Notes Block class.. Platforms: *nix

OntologyEngineI is a Perl interface a minimal Ontology implementation should satisfy. This describes the minimal interface an ontology query engine should provide. It intentionally doesnt make explicit references to the ontology being a DAG, nor does it mandate that the ontology be a... Platforms: *nix

Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::SetsBlock($block_type, $block, $verbose); Parses Sets block of NEXUS file and stores Sets data. METHODS new Title : new Usage : $block_object = new... Platforms: *nix

Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats. SYNOPSIS use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO my $parser = Bio::OntologyIO->new ( -format => "simplehierarchy", -file => "pathology_terms.csv",... Platforms: *nix

Bio::ClusterI module is a cluster Perl interface. SYNOPSIS # see the implementations of this interface for details but # basically my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members =... Platforms: *nix

Bio::NEXUS::MatrixBlock is a Perl module that provides functions for handling blocks that have matrices. SYNOPSIS This module is the super class of Characters, Unaligned, and Distances block classes, and indirectly it is a super-class of Data and History blocks, which are both sub-classes of... Platforms: *nix

The module includes a sidebar block listing the names of the users with biographies. A tiled vcard view that includes avatars can be displayed with theme_bio_tiles(). In order to display a list of biographies the function bio_list() can be called.InstallationUnpack in your modules folder... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

Any node-type can be assigned as the bio or Bio module can provide its own node type. The bio can display on the users' profile pages and/or it can add "View [username]'s [Bio]" links to nodes.Installation - Unpack in your modules folder (usually /sites/all/modules/) and enable under Administer >... Platforms: Windows, Mac, *nix, PHP, BSD Solaris

Features - Listing profiles by role - Restricting access to profiles by both who is viewing the profile and who owns the profileInstallation - Unpack in your modules folder (usually /sites/all/modules/) and enable under Administer > Site Building > Modules.  Requirements: - Drupal 5.x - Drupal... Platforms: Windows, Mac, *nix, PHP, BSD Solaris