Open Source Java Bio-Informatics Software - Page 23

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.

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.

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences

The ORIEL workbench is a data browsing interface for REST-based information retrieval services. Originally developed for Bioinformatics applications.

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.

OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.

OmniGene is a set of reausable components that have been packaged into frameworks. These frameworks are used to produce domain specific services for common bioinformatics tasks including: visualization, database access, and pipeline building.

Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations, results locations, alignments, analysis specifications and further information relevant to the experiments. The sample tracking system for oncogenomic studies (Onco-STS) is designed to store these data and make them easily accessible to the researchers who work with the samples. The system is a web application, which includes a database and a front-end web page that allows the remote access, submission and updating of the sample data in the database.

OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework.

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing complex queries against the Gene Ontology Database.

Ontologizer is an Open Source tool with the purpose of identifing enriched Gene Ontology terms in lists of names of genes or gene products.

An open source common API tasks to query existing ontology resources in local files (OWL and OBO) as well as public repositories (Bioportal, OLS) using a standardised, uniform interface.

NOTE: please refer to OPPL 2. OPPL is a preprocessor language that allows users to define macros for altering OWL ontologies. The syntax is very simple and intuitive, offering a very abstract and high level "scripting" language, for example for int

The purpose of this project is to develop ontology-based tools for the study of animal behavior (ethology). The goal is not to produce a general ontology or editor, but comparative methods and (behavior) data entry tools (ethontos and owlwatcher).

obo An umbrella organization for ontologies and structured shared controlled vocabularies for use across all biological and biomedical domains

The Open Genome Analysis Platform (OGAP) provides an effectual analysis and visualization toolset for a variety of genome, proteomics, and associated data.

A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk

Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f

OpenClinica is a web-based electronic data capture platform for clinical research. See http://www.OpenClinica.org/ for downloads, documentation, and mailing lists.

OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (text mining) application: a semantic parser for information extraction.

Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).

OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability analysis and elements of experimental design.

El proyecto central es la conformación de un Sistema de Información Hospitalaria, se pretende ir por subproyectos los cuales formaran las piezas fundamentales que se integraran mediante perfiles IHE que vayan estableciéndose para la norma HL7v3

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.