Search Results for "java on java" - Page 16

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

BAMStats is a GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

ToxOtis is a Java interface to the predictive toxicology services of OpenTox. ToxOtis is being developed to help both those who need a painless way to consume OpenTox web services and for ambitious service providers...

Populating Research Data Australia (RDA) with collection descriptions of Australian-related biomolecular data held in the European Bioinformatics Institute (EBI) databanks. This project is ANDS-funded through the DIISR Education Infrastructure Fund.

The code here is a parser for CALBC corpus into Java object.

Easy Homozygosity Profiling of Affymetrix SNP Arrays

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003

Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.

PileLine (Pileup pipeLine) is a toolkit for efficient handling of genomic position (GP) files, produced by next-generation sequencing experiments. It is designed to be memory efficient by performing on-disk operations over sorted GP files.

The Celera Genome Browser, developed at Celera Genomics as part of Celera's sequencing and annotation of the human genome, and released as open source in 2006.

A computational tool to design and annotate metabolic pathways from genome annotations

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.

This is an independent fork of the ensj-core Ensembl Java API. This version of the API does not receive support from Ensembl. The project is still available under the original LGPL license.

VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.

Data curation tool to maintain variables for the National Survey of Health and Development managed by the Lifelong Health and Ageing Unit of the Medical Research Council.

Web application to make user-friendly requests on large XML database. Tools to XML-ize large bodies of semi-formal texts (like floras). Computer-assisted specimen identification. Uses natural language processing, 2D/3D images analysis and generation.

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)

SyMBA is a Data Archive and Integrator that is based on the Functional Genomics Object Model (http://fuge.sf.net) and which archives, stores, and retrieves raw high-throughput data. See http://symba.sf.net and http://www.cisban.ac.uk

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.

The creation of quantitative SBML models is a time-intensive manual process. Saint, an automated SBML annotation integration tool, aids the modeller and reduces development time by providing information about a model in an easy-to-use interface.

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.