Simple Bio Data

Marshals simple Python data types into a custom XML format. The Marshaller and Unmarshaller classes can be subclassed in order to implement marshalling into a different XML DTD. Original Authors are XML-SIG. It is fully compatible with PyXML implementation, enable namespace support for XML...

Text::VimColor is a syntax color text in HTML or XML using Vim. SYNOPSIS use Text::VimColor; my $syntax = Text::VimColor->new( file => $0, filetype => perl, ); print $syntax->html; print $syntax->xml; This module tries to markup text files according to their syntax. It can be used to...

Triangle Wizard is a free hack 'n slash game featuring retro graphics and a wealth of content. You are a wizard (of a selectable profession, e.g. Necromancer, Shadow Adept, Sunmage, etc.) and need to travel through 100+ dungeon levels and many different environments in order to defeat your...


Platforms: Windows

HxD is a carefully designed and fast hex editor which, additionally to raw disk editing and modifying of main memory (RAM), handles files of any size. The easy to use interface offers features such as searching and replacing, exporting, checksums/digests, insertion of byte patterns, a file...


Platforms: Windows

Bashup is an easy to use but complex shell script for automating backups. It is designed to have a minimum set of requirements (e.g. no external language interpreter like ruby, python, perl). It provides you with tasks for backing up directories, mysql, postgresql, oracle and subversion data,...


Platforms: *nix

Simple Data Backup is a FREE program that allows you to quickly and easily back up an entire folder structure from one drive to another. In addition, you can have the program automatically back up certain folders every so many days. It is a simple, but effective program at maintaining a backup of...


Platforms: Windows

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

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::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::Genex::Software is Perl module with methods for processing data from the GeneX DB table: Software. SYNOPSIS use Bio::Genex::Software; # instantiating an instance my $Software = Bio::Genex::Software->new(id=>47); # retrieve data from the DB for all columns $Software->fetch(); #...


Platforms: *nix

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

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

Declare::Constraints::Simple is a Perl module for Declarative Validation of Data Structures. SYNOPSIS use Declare::Constraints::Simple-All; my $profile = IsHashRef( -keys => HasLength, -values => IsArrayRef( IsObject )); my $result1 = $profile->(undef); print $result1->message, "n"; #...


Platforms: *nix

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...


Platforms: *nix

Bio::NEXUS::DataBlock is a Perl module that represents the deprecated DATA Block in NEXUS file. SYNOPSIS $block_object = new Bio::NEXUS::DataBlock($type, $block, $verbose, $taxlabels_ref); The DataBlock class represents the deprecated Data Block in a NEXUS file. Data Blocks are still used...


Platforms: *nix

Simple Data Grid can be used to display MySQL database query result data in an HTML table grid.There are classes to define details of the headers and body of table grid. There is also a class for executing MySQL database queries and return the results in a bi-dimensional array.The data grid...


Platforms: PHP

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an...


Platforms: *nix

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

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

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #...


Platforms: *nix