Search Results for "using" - Page 3

An api for domain level interaction with SNOMED CT and an implementation based on a storage engine using a native SNOMED distribution stored in neo4j as a backend.

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.

A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition.

EvoPromoter is a JAVA application that detects promoter regions in aligned nucleotide sequences using phylogenetic hidden markov models.

SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and ability to export results in the standard formats of the area.

Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex

A new open-source tool that integrates pipeline automated identification and phylogenetic studies of microbial communities using genes sequences

Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.

Contemplate is a bioinformatics tool for finding cis-regulatory modules (CRMs) in noncoding genomic regions using comparative sequence data.

A phologenetic supertree construction/assembly tool using triplet similarity as the objective function.

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.

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).

Corra [BMC Bioinformatics 2008] is a computational framework & tools for discovery proteomics using label free LC-MS and ATAQS [BMC Bioinformatics 2011] is a computational framework & tools for validation proteomics using SRM LC-MS method.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

JHeatChart is a simple Java library for generating heat map charts.

IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.

Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .

CNV Workshop is a web-enabled platform for analyzing genome variation such as copy number variation (CNV). Learn about CNV Workshop in our associated BMC Bioinformatics manuscript: http://www.biomedcentral.com/1471-2105/11/74

The development and curation of a range of XML-based tools for using Chemical Markup Language (CML), including XSD XML Schemas for validation, datatyping and constraining CML documents and XSLT Stylesheets for transforming, filtering and rendering.

GEM is a computational method for identification of transcription factor modulators, using expression datasets. The method tests if the correlation between factor and target gene depends on the expression of the modulator.

A sorting tool for Bioinformatics, Biochemistry and/or Molecular biology. This sorts nucleotide sequences aligned using "ClustalW". There may be a way to do this w/ original app, but someone I know couldn't figure out how - thus this project was born

The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.

The MML Framework is a temporal-spatial biological model representation language. The MML Project provides the application tool set which facilitates the goals of representing biological models using the MML specifications.

E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.