Amigo Gene Ontology

Tools designed to assist in creating and using the RadLex ontology (http://www.radlex.org).

RmiR is an R package for the analysis of microRNA and gene expression microarrays.The package is designed to coupling microRNA and gene expression data, using different databases, like TargetScan, mirBase, picTar,TarBase and others...

RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).


Platforms: Windows, Mac, Linux

Semtinel is an application framework for the semi-automatic creation, maintenance and analysis of hierarchical concept schemes (thesaurus, classification or ontology). Semtinel supports the development of new analysis methods and visualization techniques


Platforms: Windows, Mac, Linux

A simple tool for sketching out ontology structures, including OWL export. Developed at the University of Manchester as a third-year project.


Platforms: Windows, Mac, Linux

SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.


Platforms: *nix

WSMO Studio is a Semantic Web Service and Semantic Business Process modelling environment based on the Web Services Modelling Ontology (WSMO). WSMO Studio is available as a set of Eclipse plug-ins that can be extended and customised by 3rd parties.


Platforms: Windows, Mac, Linux

In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed...


Platforms: Matlab

This user interface allows a user to load some Affymetrix data in an Excel file and perform some basic operations on it - log transform, log ratio, normalization, noise reduction, filtering, PCA and clustering, in addition to some visualizations like profile plots, boxplots and matrix...


Platforms: Matlab

GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description...


Platforms: Matlab

General implementation of matlab version of Viterbi algorithm specifically written for gene structure finding problem in mind. However, it can be modified to suit the goal of a user.Input:Transition Probability MatrixEmission Probability MatrixInitial Probability MatrixStates Matrix (ie....


Platforms: Matlab

The SMW OntologyEditor is an extension of SemanticMediaWiki and has been developed as part of the ACTIVE project in order to enable the development of lightweight ontologies and to provide knowledge repair algorithms.


Platforms: PHP

OntoCreator is a tool able to automatically create synthetic ontologies according to user given adjustable specifications with respect to size, distribution of certain language construct and expressivity. The current version will generate ontologies according to the ?*a*ffnet einen externen Link...


Platforms: Mac

Recent studies describe that the level of gene expression between species is positively correlated with the time that has passed since the species split from a common ancestor (Ranz et al., 2006). Moreover, Khaitovich et al. (2004) found a linear relationship between divergence time and...


Platforms: Mac

Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.


Platforms: Mac

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.


Platforms: Mac

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.


Platforms: *nix

NetAtlas is a Cytoscape plugin that uses tissue gene expression data to filter cellular signaling network. The plugin identifies of tissue-defined networks, tissue-specific network components, and components with correlated expression across tissues.


Platforms: *nix

Abuse is so good that some specialists consider it to be a 2D version of the legendary Doom. Full of powerful weapons, missiles, aliens and excellent illumination effects, the only difference is that Abuse plays in 3rd person, while Doom plays in 1st.The argument of the game is this: you are the...


Platforms: Windows

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