Search Results for "java open source" - Page 56

pISTil (a Pipeline for Interaction Sequence Tag identification and analysis) is a collection of scripts, and programs - running on both Linux and MacOS X systems - for fast analysis of large yeast two-hybrid sequence datasets.

Systems biology Php library, is an easy to use, a set of libraries used in different web site solutions which include (but not limited to) SBML, SBGN, MathML, SVG and Silverlight in Windows, XHTML, Ajax, ORM's. Suitable for any portal, systems biology

An implementation of the Markovian Jensen Shannon divergence (MJSD). The code recursively segments a sequence of symbols and then assesses the divergence of each segment with respect to the entire sequence.

Jazoo. The Zoo of virtual evolving creatures. Mostly focused on evolving communication between intelligent agents. It's in VERY early stage. Everyone's invited to join, participate, suggest, discuss etc.

RF++ is a Random Forest-based classifier. It can classify cluster-correlated non-independent data in a statistically valid fashion. RF++ also identifies important variables (biomarkers) in datasets with large numbers of variables and few subjects.

This project supports ASTM E13.15 "Analytical Data Magement" in its work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry and biology data.

Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. ...

The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis

Collection of tools for performing robust case-control disease and quantitative trait association studies using Copy Number Variants- Latest version should now be downloaded from Bioconductor

EXtensible Instrument Processing Protocol (XIPP) is used to query, configure, and stream data between XIPP-enabled instruments and personal computers on dedicated instrument networks using UDP packets. Cross-platform, C/C++.

This is a Perl module for doing snp analysis based on shotgun sequencing reads and a reference genome sequence. Its primary input is the cigar alignment format outputted from ssaha2.

ChIPOTle is a peak-finding algorithm used to analyze ChIP-chip microarray data

This project shows how to integrate NVIDIA CUDA GPU programming API into ITK (Insight Segmentation and Registration Toolkit) library

BioShears is GUI Restriction Enzymes Database Program Programed by C++ using Qt 4 this program is free software; you can redistribute it and/or modify it under the terms of the GNU GENERAL PUBLIC LICENSE with my best regards Osama S Alrawab

GOCART is a modular open-source application used to assemble biological sequences into Gene Ontology (GO) annotated contigs for Web GUI visualization based on their corresponding hierarchal GO structure, described by the Gene Ontology Consortium.

HZL Beta 2 is the updated version of a software application based on MS-Access, designed to manage and digitize botanical and zoological collections.

The Chemical Structures Project is a set of 3D structures of molecules in CML format. Each file contains also some physical properties, which can be access using a web browser or a CML file reader.

A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.

Cyrille is an workflow management system aimed at high throughput pipelines in Bioinformatics.

mzSquash is a compression tool for mzML files, an XML-based standard developed by HUPO PSI (http://www.psidev.info) for spectrometer output. All development has ceased. The tool may be useful educationally, but is not a recommended utility.

RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

ICRPfinder finds or generates DNA patterns which can include restriction enzyme recognition sites in coding sequences without changing the translated protein sequence.

NoBlast provides a new extended user friendly csv output format and offers an option to correct the statistics when split databases are used for NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and Tblastx).

TiMAT2 contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.