Amigo 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|
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...
|License: Freeware||Size: 21.13 MB||Download (16): ErmineJ Download|
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
|License: Freeware||Download (49): FastSemSim Download|
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...
|License: Freeware||Size: 870.4 KB||Download (105): GO::View Download|
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....
|License: Freeware||Download (73): MEFIT Download|
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|
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...
|License: Freeware||Size: 4.1 KB||Download (20): Blast2GO Download|
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...
|License: Freeware||Size: 2.4 MB||Download (7): EcoCyc Download|
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...
|License: Freeware||Size: 4.7 MB||Download (85): 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(...
|License: Freeware||Size: 4.7 MB||Download (76): Bio::Ontology::GOterm 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 =...
|License: Freeware||Size: 4.7 MB||Download (74): Bio::Ontology::Ontology Download|
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...
|License: Freeware||Size: 1.1 MB||Download (76): GENE Graph Export Engine Download|
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...
|License: Freeware||Size: 4.7 MB||Download (71): Bio::Ontology::OntologyEngineI Download|
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|
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|
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.
|License: Freeware||Size: 28.43 MB||Download (16): ORE (Ontology Rule Editor) Download|
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...
|License: Freeware||Size: 4.54 MB||Download (297): Advanced Pathway Painter Download|
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)...
|License: Freeware||Size: 8.19 KB||Download (86): Bio::SAGE::Comparison Download|
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" ); #...
|License: Freeware||Size: 19.46 KB||Download (76): Bio::SAGE::DataProcessing Download|
MeV or Multiple Experiment Viewer is a Java tool to help you with microarray gene expression data analysis. MeV supports 5 input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery.
|License: Freeware||Size: 64.1 MB||Download (60): MeV 4.6.2 Download|