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Amigo Gene Ontology freeware
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Amigo Gene Ontology

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Released: December 19, 2012  |  Added: December 19, 2012 | Visits: 348

Gene Ontology The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more. Platforms: Windows, Mac, Linux

License: Freeware Size: 44.5 MB Download (29): Gene Ontology Download

Released: June 24, 2012  |  Added: June 24, 2012 | Visits: 242

BioAGENDA AGENDA (Application for mining Gene Ontology Data) Platforms: Windows, Mac, Linux

License: Freeware Size: 59.32 KB Download (27): BioAGENDA Download

Added: July 09, 2013 | Visits: 222

ErmineJ ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac

License: Freeware Size: 21.13 MB Download (16): ErmineJ Download

Released: July 19, 2012  |  Added: July 19, 2012 | Visits: 316

FastSemSim FastSemSim is specially designed as a handy Python-based efficient implementation of a couple of semantic similarity measures. The main target of the project is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology Platforms: Windows

License: Freeware Download (48): FastSemSim Download

Added: April 23, 2010 | Visits: 731

GO::View GO::View is a Perl module that creates a gif or png image for visualizing the GO DAG. This perl module generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the GO::TermFinder perl module created by the Stanford... Platforms: *nix

License: Freeware Size: 870.4 KB Download (105): GO::View Download

Released: October 19, 2012  |  Added: October 19, 2012 | Visits: 249

MEFIT MEFIT, also known as the Microarray Experiment Functional Integration Technology is developed as a system for microarray integration. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions.... Platforms: Windows

License: Freeware Download (71): MEFIT Download

Released: October 12, 2012  |  Added: October 12, 2012 | Visits: 269

Osprey Network Visualization System Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID. Platforms: Windows, Mac, Solaris, Linux

License: Freeware Size: 8.32 MB Download (31): Osprey Network Visualization System Download

Added: September 12, 2013 | Visits: 203

Blast2GO Blast2GO?*A* is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Main Application Features are: Easy start up and low maintenance. Make sure you have JAVA, download Blast2GO from this site and start using the application. Updates are... Platforms: Mac

License: Freeware Size: 4.1 KB Download (19): Blast2GO Download

Released: March 27, 2014  |  Added: March 27, 2014 | Visits: 155

EcoCyc EcoCyc is an electronic reference source for E. coli biologists and biologists who work with related microorganisms. EcoCyc Mobile provides a streamlined mobile interaction for EcoCyc, a bioinformatics database that describes the genome and the biochemical machinery of Escherichia coli K-12... Platforms: iOS

License: Freeware Size: 2.4 MB Download (7): EcoCyc Download

Added: February 01, 2010 | Visits: 776

Bio::Ontology::Relationship 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 (85): Bio::Ontology::Relationship Download

Added: July 21, 2010 | Visits: 568

Bio::Ontology::GOterm 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 (76): Bio::Ontology::GOterm Download

Added: November 21, 2010 | Visits: 464

Bio::Ontology::Ontology 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 (74): Bio::Ontology::Ontology Download

Added: January 25, 2010 | Visits: 825

GENE Graph Export Engine GENE Graph Export Engine is an advanced XML exporter. GENE Graph Export Engine is a complex convertor/framework for multi-namespace XML transforming and exporting. It is able to convert various XML types including SVG, DocBook, MathML, XSL-FO, and their combinations into a wide area of output... Platforms: *nix

License: Freeware Size: 1.1 MB Download (76): GENE Graph Export Engine Download

Added: July 15, 2010 | Visits: 509

Bio::Ontology::OntologyEngineI 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

License: Freeware Size: 4.7 MB Download (71): Bio::Ontology::OntologyEngineI Download

Released: October 24, 2012  |  Added: October 24, 2012 | Visits: 412

Gene Visualizer Gene Visualizer is a small app designed to display an organism's genes visually. The program takes two sets of genes as input. One is a list of an organism's predicted genes, and the other is a list of an organism's known genes. It can be useful to compare how the two lists of genes match up,... Platforms: Windows

License: Freeware Download (69): Gene Visualizer Download

Added: May 10, 2013 | Visits: 197

Experimental Factor Ontology It is an application focused on the ontology modeling ot the experimental factors in ArrayExpress.The application is used also in the constructing of mappings to multiple existing domain specific ontologies, such as Disease Ontology. Platforms: Windows, Mac, *nix, Perl, BSD Solaris

License: Freeware Download (29): Experimental Factor Ontology Download

Added: May 10, 2013 | Visits: 344

Perl Entrez Gene Parser This program is a parser that abstract a data structure from a given Entrez Gene record, and users of the parser can decide what to do/extract from the data structure. Perl Entrez Gene Parser project provides Perl parsers for NCBI's Entrez Gene based on regular expression, Parse::RecDescent,... Platforms: Windows, Mac, *nix, Perl, BSD Solaris

License: Freeware Download (41): Perl Entrez Gene Parser Download

Added: July 16, 2013 | Visits: 210

ORE (Ontology Rule Editor) ORE (Ontology Rule Editor) is a platform-independent application to manage the use of inference rules defined on a model represented by an ontology. ORE offers a easy, well-guided and intiutive GUI to define and test these inference rules. Platforms: *nix

License: Freeware Size: 28.43 MB Download (16): ORE (Ontology Rule Editor) Download

Released: August 30, 2010  |  Added: September 03, 2010 | Visits: 4.804

Advanced Pathway Painter This freeware program visualizes pathways (KEGG, BioCarta, GenMAPP, ...). The user has the possibility to display any kind of quantitative data from gene and protein experiments directly within the pathways (colours represent the value). The linking between the pathway items and the experiment... Platforms: Windows

License: Freeware Size: 4.54 MB Download (297): Advanced Pathway Painter Download

Added: May 09, 2010 | Visits: 771

Bio::SAGE::Comparison 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

License: Freeware Size: 8.19 KB Download (86): Bio::SAGE::Comparison Download

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