Bio Informatics Tool
Bio::Ontology::Relationship is a relationship for an ontology. SYNOPSIS $rel = Bio::Ontology::Relationship->new( -identifier => "16847", -subject_term => $subj, -object_term => $obj, -predicate_term => $pred ); This is a basic implementation of Bio::Ontology::RelationshipI. The...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (109): Bio::Ontology::Relationship Download |
Bio::Ontology::GOterm is a representation of GO terms. SYNOPSIS $term = Bio::Ontology::GOterm->new ( -go_id => "GO:0016847", -name => "1-aminocyclopropane-1-carboxylate synthase", -definition => "Catalysis of ...", -is_obsolete => 0, -comment => "" ); $term->add_definition_references(...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (95): Bio::Ontology::GOterm Download |
WebInject is a free tool for automated testing of web applications and services. It can be used to test individual system components that have HTTP interfaces (JSP, ASP, CGI, PHP, Servlets, HTML Forms, etc), and can be used as a test harness to create a suite of [HTTP level] automated functional,...
Platforms: *nix
License: Freeware | Size: 29.7 KB | Download (102): WebInject - Web/HTTP Test Tool Download |
Bio::ConnectDots::ConnectDots is a top level class for connect-the-dots. SYNOPSIS use Bio::ConnectDots::DB; use Bio::ConnectDots::ConnectDots; my $db=new Bio::ConnectDots::DB(-database=>test, -host=>computername, -user=>usename, -password=>secret); my $cd=my $cd=new...
Platforms: *nix
License: Freeware | Size: 102.4 KB | Download (98): Bio::ConnectDots::ConnectDots Download |
DREAM Tool is a generic framework that aims at providing a common semantic domain which can express several (real-time, power consumption, resource) constraints. The semantic domain has an executable C++ model which has been semantically anchored to the hybrid automata formalism. Although the...
Platforms: *nix
License: Freeware | Size: 3.3 MB | Download (140): DREAM Tool 0.7 Download |
The mii-tool command provides an tool for checking and setting ethernet cabling parameters. It is normally included in Bernd Eckenfels net-tools package, but this is an single distribution which only contains mii-tool. This package also comes with cleaned makefile and allows build-time...
Platforms: *nix
License: Freeware | Size: 15.36 KB | Download (273): mii-tool Download |
Sudoku Tool is a sudoku game that helps you to solve sudoku puzzles. Sudoku Tool can generate puzzles randomly or puzzles can be entered manually. Some of the features include random puzzle generation, pencil marks, and the ability to save games. Manual Setup: The game starts in...
Platforms: *nix
License: Freeware | Size: 1.5 MB | Download (106): Sudoku Tool Download |
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
License: Freeware | Size: 4.7 MB | Download (95): Bio::AnnotationCollectionI Download |
Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (98): Bio::Seq Download |
Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq. SYNOPSIS # Bio::PrimarySeqI is the interface class for sequences. # If you are a newcomer to bioperl, you should # start with Bio::Seq documentation. This # documentation is mainly for developers using # Bioperl. #...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (92): Bio::PrimarySeqI Download |
Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx =...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (100): Bio::Index::Swissprot Download |
MIME-tool is a little mime encoding tool I slapped together when I needed something on a production box at work (productions = no C development environment, only the ancient K&R compiler required for god-knows-what sys-admin task). The resulting program will compile happilly on both the...
Platforms: *nix
License: Freeware | Size: 13.31 KB | Download (117): MIME-tool Download |
Babel Interoperability Tool is a tool for mixing C, C++, Fortran77, Fortran90, Python, and Java in a single application. This is our cornerstone product, representing 90% of our effort. Babel is the foundation for a multilanguage scientific compoenent framework. We are often called "The Babel...
Platforms: *nix
License: Freeware | Size: 13.1 MB | Download (96): Babel Interoperability Tool Download |
Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (127): Bio::Tools::CodonTable Download |
Bio::Map::CytoMap is a Bio::MapI compliant map implementation handling cytogenic bands. SYNOPSIS use Bio::Map::CytoMap; my $map = new Bio::Map::CytoMap(-name => human1, -species => $human); foreach my $marker ( @markers ) { # get a list of markers somewhere $map->add_element($marker); }...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (124): Bio::Map::CytoMap Download |
Bio::Biblio::Patent is a representation of a patent. SYNOPSIS $obj = new Bio::Biblio::Patent (-doc_number => 1-2-3-4-5); #--- OR --- $obj = new Bio::Biblio::Patent; $obj->doc_number (1-2-3-4-5); A storage object for a patent. See its place in the class hierarchy in...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (96): Bio::Biblio::Patent Download |
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
License: Freeware | Size: 4.7 MB | Download (92): Bio::Ontology::Ontology Download |
Bio::Factory::SeqAnalysisParserFactoryI is a Perl interface describing objects capable of creating SeqAnalysisParserI compliant parsers. SYNOPSIS # initialize an object implementing this interface, e.g. $factory = Bio::Factory::SeqAnalysisParserFactory->new(); # obtain a parser object...
Platforms: *nix
License: Freeware | Size: 4.7 MB | Download (97): Bio::Factory::SeqAnalysisParserFactoryI Download |
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
License: Freeware | Size: 4.7 MB | Download (90): Bio::Location::CoordinatePolicyI Download |
Bio::Tools::Run::PiseApplication::freak is a Perl module. Bio::Tools::Run::PiseApplication::freak Bioperl class for: FREAK Residue/base frequency table or plot (EMBOSS) Parameters: (see also: http://bioweb.pasteur.fr/seqanal/interfaces/freak.html for available values): freak...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (94): Bio::Tools::Run::PiseApplication::freak Download |