Amigo Gene Ontology

Arastreju is a Java based engine for ontology based information management.

Docgen plugin for Protege provides a quick export of all the content of an ontology (classes, instances and documentation) in various formats (html, pdf, fo...). Images, Graphs, URL are readyly included in reports.

Dogwood is an ontology-aware Distributed Annotation System (DAS) server framework for the integration of biological, biomedical and clinical data.


Platforms: Windows, Mac, Linux

EPTable is a simple web-based tool to analyze microarray gene expression profiles with additional gene profiles.


Platforms: Mac, BSD, Linux

Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.


Platforms: Windows, Mac, Linux

EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries and provides several layers of annotation based on Entrez Gene to allow the user to highlight useful genes and manage cDNA library projects.


Platforms: Windows, Mac, Linux

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.


Platforms: Windows, Mac, Linux

Hawthorn provides a caching and lookup mechanism for bioinformatics ontology formats such as OBO and DAG.


Platforms: Windows, Mac, Linux

HERAKLES is a reasoning broker framework for OWL (Web Ontology Language) reasoning systems.


Platforms: Windows, Mac, Linux

IGBM (Identification of gene blocks in microorganisms) implements a BLAST-like method to infer conserved gene clusters among closely related prokaryotes, and provides a graphical user interface to navigate the identified clusters and their annotated info


Platforms: Windows, Mac, Solaris, Linux

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms).


Platforms: Windows, Mac, Linux

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.


Platforms: Windows, Mac, Linux

Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.


Platforms: Windows, Mac, Linux

MapPSO is a tool for Ontology Alignment, which uses Discrete Particle Swarm Optimisation. A particle swarm is used to search for the optimal alignment. The algorithm is massively parallel and adapts naturally on parallel architectures.


Platforms: Windows, Mac, Linux

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)


Platforms: Windows, Mac, Linux

OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses.


Platforms: Windows, Mac, Linux

Ontology visualization plugin for Protege in an interactive 3D space.


Platforms: Windows, Mac, Linux

OSGI4AMI Ontology (http://www.booksonline.iospress.nl/Content/View.aspx?piid=13894) describes devices properties and behavior. Several implementations will be available. Universidad de Zaragoza Java Interfaces Reference Implementation and osgi bundle


Platforms: Windows, Mac, Linux

The Program to Assemble Spliced Alignments (PASA) is used to automatically incorporate ESTs and full-length cDNAs into gene structure annotations, in the process annotating UTRs, alternative splicing variations, and polyadenylation sites.


Platforms: Mac, BSD, Linux

A SOA-based framework for multilingual question answering (QA) systems that answer natural language questions with the help of a domain ontology and structured answer data sources from freely specifiable domains.


Platforms: Windows, Mac, Linux