Bio Node
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
License: Freeware | Download (57): Bio Jeff Robbins Download |
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
License: Freeware | Download (55): Bio role terms Download |
Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees. SYNOPSIS new Bio::NEXUS::Node; METHODS new Title : new Usage : $node = new Bio::NEXUS::Node(); Function: Creates a new Bio::NEXUS::Node object Returns : Bio::NEXUS::Node object Args : none...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (98): Bio::NEXUS::Node Download |
Bio::Tree::NodeNHX is a Simple Tree Node with support for NHX tags. SYNOPSIS use Bio::Tree::NodeNHX; my $nodeA = new Bio::Tree::NodeNHX(); my $nodeL = new Bio::Tree::NodeNHX(); my $nodeR = new Bio::Tree::NodeNHX(); my $node = new Bio::Tree::NodeNHX(); $node->add_Descendents($nodeL);...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (114): Bio::Tree::NodeNHX Download |
Bio::Graph::SimpleGraph is a Perl module that can create and manipulate undirected graphs. SYNOPSIS use Bio::Graph::SimpleGraph; my $graph=new SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
Platforms: *nix
License: Freeware | Size: 5.6 MB | Download (107): Bio::Graph::SimpleGraph Download |
Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The...
Platforms: *nix
License: Freeware | Size: 99.33 KB | Download (95): Bio::Network::IO::dip_tab Download |
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
License: Freeware | Size: 153.6 KB | Download (91): Bio::NEXUS::TreesBlock Download |
Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa. SYNOPSIS use Bio::Tree::Compatible; use Bio::TreeIO; my $input = new Bio::TreeIO(-format => newick, -file => input.tre); my $t1 = $input->next_tree; my $t2 = $input->next_tree; my...
Platforms: *nix
License: Freeware | Size: 5.6 MB | Download (94): Bio::Tree::Compatible Download |
Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character). SYNOPSIS new Bio::NEXUS::WeightSet($name, @weights, $iswt); A module representing column weights in alignment (for each character) METHODS new Title : new Usage : $node = new...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (89): Bio::NEXUS::WeightSet Download |
Bio::ConnectDots::SimpleGraph is a simple, hopefully fast undirected graph package. SYNOPSIS use SimpleGraph; my $graph=new Bio::ConnectDots::SimpleGraph; # read pairs of nodes from STDIN while (<>) { my($node1,$node2)=split; $graph->add_edge($node1,$node2); } my @nodes=graph->nodes;...
Platforms: *nix
License: Freeware | Size: 102.4 KB | Download (93): Bio::ConnectDots::SimpleGraph Download |
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
License: Freeware | Size: 102.4 KB | Download (90): Bio::Phylo::Treedrawer::Svg Download |
Bio::Phylo::IO Perl module contains input and output of phylogenetic data. SYNOPSIS use Bio::Phylo::IO; # parsing a tree from a newick string my $tree_string = (((A,B),C),D);; my $tree = Bio::Phylo::IO->parse( -string => $tree_string, # old parser, always adds node labels -format =>...
Platforms: *nix
License: Freeware | Size: 143.36 KB | Download (97): Bio::Phylo::IO 0.17 Download |
Have you ever wanted to include the rendering of node within the content of another node? For example, embedding an Image/Slideshow/Video node within the body of an Article node. Or the embedding of an Author node as a bio block within a blog posting? Node Embed allows you to do that.Node Embed...
Platforms: PHP
License: Freeware | Size: 10 KB | Download (45): Node Embed Download |
Bio::Graphics::Glyph::alignment is the "alignment" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This is identical to the "graded_segments" glyph, and is used for drawing features that consist of discontinuous segments. The color intensity of each segment is...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (99): Bio::Graphics::Glyph::alignment Download |
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
License: Freeware | Size: 4.7 MB | Download (86): Bio::OntologyIO::simplehierarchy Download |
Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods. A workflow is defined by a set of methods which all instanciate the class PiseApplication. SYNOPSIS # First, create a Bio::Tools::Run::AnalysisFactory::Pise object: my $factory = new...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (97): Bio::Tools::Run::PiseWorkflow Download |
Bio::Tools::AlignFactory is a base object for alignment factories. SYNOPSIS You wont be using this as an object, but using a dervied class like Bio::Tools::pSW Holds common Alignment Factory attributes in place.
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (165): Bio::Tools::AlignFactory Download |
Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families. SYNOPSIS use Bio::Tools::Run::TribeMCL; use Bio::SearchIO; # 3 methods to input the blast results # straight forward raw blast output (NCBI or WU-BLAST) my @params =...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (213): Bio::Tools::Run::TribeMCL Download |
Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class). SYNOPSIS This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other...
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (91): Bio::NEXUS::Block Download |
Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file. SYNOPSIS if ( $type =~ /taxa/i ) { $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose); } If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data....
Platforms: *nix
License: Freeware | Size: 153.6 KB | Download (93): Bio::NEXUS::TaxaBlock Download |