Bio Rhythm App
App::SimpleScan::Plugin::Forget is a Perl module to forget a variables value. SYNOPSIS # In a simple_scan input file, after installing this module: # Define the variable foo: %%var foo baz bar quux # Later in the file: %%forget foo # foo is now undefined, and will not be replaced...
Platforms: *nix
License: Freeware | Size: 4.1 KB | Download (88): App::SimpleScan::Plugin::Forget Download |
App::SimpleScan::Cookbook is a documentation-only module that describes how to use simple_scan for some common Web testing problems. BASICS simple_scan reads test specifications from standard input and generates Perl code based on these specifications. It can either execute them immediately,...
Platforms: *nix
License: Freeware | Size: 54.27 KB | Download (92): App::SimpleScan::Cookbook Download |
Bio::LiveSeq::Translation is a translation class for LiveSeq. This stores informations about aminoacids translations of transcripts. The implementation is that a Translation object is the translation of a Transcript object, with different possibilities of manipulation, different coordinate...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (104): Bio::LiveSeq::Translation Download |
Bio::Tools::Run::JavaRunner is a Perl module that can run java programs. SYNOPSIS my $runner = Bio::Tools::Run::JavaRunner->new(-jar => $jar); $runner->run(); This module is probably incomplete. It is intended to be a wrapper for running java programs..
Platforms: *nix
License: Freeware | Size: 942.08 KB | Download (96): Bio::Tools::Run::JavaRunner Download |
Bio::Graphics::Glyph::cds module contains the "cds" glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (95): Bio::Graphics::Glyph::cds Download |
Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;...
Platforms: *nix
License: Freeware | Size: 5.7 MB | Download (99): Bio::Graphics::Panel 1.5.2_005 Download |
Bio::Graphics::Feature is a simple feature object for use with Bio::Graphics::Panel. SYNOPSIS use Bio::Graphics::Feature; # create a simple feature with no internal structure $f = Bio::Graphics::Feature->new(-start => 1000, -stop => 2000, -type => transcript, -name => alpha-1...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (100): Bio::Graphics::Feature Download |
Bio::DB::Flat::BDB::swissprot is a swissprot adaptor for Open-bio standard BDB-indexed flat file. SYNOPSIS See Bio::DB::Flat. This module allows swissprot files to be stored in Berkeley DB flat files using the Open-Bio standard BDB-indexed flat file scheme. You should not be using this...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (136): Bio::DB::Flat::BDB::swissprot Download |
Bio::Graphics::Glyph::minmax is the minmax glyph. SYNOPSIS See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >. This glyph is the common base class for Bio::Graphics::Glyph::graded_segments and Bio::Graphics::Glyph::xyplot. It adds an internal method named minmax() for calculating...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (115): Bio::Graphics::Glyph::minmax Download |
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. SYNOPSIS use Bio::Graphics::FeatureFile; my $data = Bio::Graphics::FeatureFile->new(-file => features.txt); # create a new panel and render contents of the file onto it my $panel = $data->new_panel; my...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (99): Bio::Graphics::FeatureFile Download |
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
License: Freeware | Size: 4.7 MB | Download (92): Bio::DB::GFF::Feature Download |
Bio::Biblio is a Bibliographic Query Service module. SYNOPSIS use Bio::Biblio; my $biblio = new Bio::Biblio; print $biblio->find (perl)->get_count . "n"; my $collection = $biblio->find (brazma, authors); while ( $collection->has_next ) { print $collection->get_next; } #The new()...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (101): Bio::Biblio 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::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::Affymetrix::CDF is a Perl module to parse Affymetrix CDF files. SYNOPSIS use Bio::Affymetrix::CDF; # Parse the CDF file my $cdf=new Bio::Affymetrix::CDF({"probemode"=>0}); $cdf->parse_from_file("foo.cdf"); # Find some fun facts about this chip type print...
Platforms: *nix
License: Freeware | Size: 64.51 KB | Download (120): Bio::Affymetrix::CDF Download |
AxKit::App::Gallery works by generating XML, and then passing the generated XML through a collection of stylesheets. The output of one stylesheet is passed on as input to the next. In this way, a pipeline of stylesheets if formed. Some of the stylesheets are written in XSLT, some are written in...
Platforms: *nix
License: Freeware | Size: 26.62 KB | Download (91): AxKit::App::Gallery::stylesheets Download |
CGI::Ex::App is a anti-framework application framework. Fill in the blanks and get a ready made web application. This module is somewhat similar in spirit to CGI::Application, CGI::Path, and CGI::Builder and any other "CGI framework." As with the others, CGI::Ex::App tries to do as much of the...
Platforms: *nix
License: Freeware | Size: 215.04 KB | Download (100): CGI::Ex::App Download |
Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class, as in: use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq); $aln = $in->next_aln(); This object can create...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (129): Bio::AlignIO::bl2seq Download |
Bio::AlignIO::msf is a Perl module with msf sequence input/output stream. SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. This object can transform Bio::Align::AlignI objects to and from msf flat file databases. The rest of the documentation details each of...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (96): Bio::AlignIO::msf Download |
Bio::GMOD::Admin::Monitor::blat is a Perl module that can monitor a BLAT server. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $gmod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $gmod->live_version; Update a MOD installation...
Platforms: *nix
License: Freeware | Size: 71.68 KB | Download (106): Bio::GMOD::Admin::Monitor::blat Download |