Search Results for "java open source projects" - Page 2

Many biological laboratories dealing with genomic samples are facing the problem of sample tracking, both for pure laboratory management and efficiency, and for internal policies, such as Good Laboratory Practices (GLP). Our laboratory exploits PCR techniques and next-generation sequencing (NGS) methods, to perform high-throughput integration site monitoring in different clinical trials and scientific projects, based on the delivery of therapeutic genes by viral vectors integrating into the...

A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

A collection of tools to transform common biosequence formats (e.g. EMBL, SWISS-PROT, UniProtKB, GenBank and RefSeq) into the fasta sequence format.

This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.

NanoTrackJ moved to GitHub! Please see: https://github.com/thorstenwagner/ij-nanotrackj or http://fiji.sc/NanoTrackJ

NMR Spectroscopy tools. See http://connjur.uchc.edu

The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.

ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.

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...

The TIMTAM (Target Information Management Tracking And More) system implements a secure knowledgebase supporting the management, tracking, and analysis of experimental data associated with structural biology projects.

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

gfit creates an interface between computational models and experimental data and provides tools for their analysis

SARSE is a scientific data editor that uses the extendable column format, allows interactive overview, tracks editing history, and has a user extendable tool box.

A Collection of STAR/CIF processing libraries and related tools, including sub-projects: AStar, TEStar and others...

MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.

Client tools for the FuncNet protein function analysis platform: http://funcnet.eu/

VoltIJ (for VOLume viewing Tools for ImageJ) is a plugin for ImageJ allowing the 3D visualization of volumetric scalar data.

molecular simulation program for anisotropic particle shape and potential

primeHandle is a set of data management tools in support of the PrIMe Initiative (http://primekinetics.org). primeHandle includes graphical user interfaces for searching through data collections, editing and submitting data to the PrIMe Data Depository.

NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.

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

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)