Search Results for "core java"

nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a...

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. Experiment platforms supported include Illumina HiSeq, MiSeq, iScan, ABI Sanger sequencing,...

We present ERNE (Extended Randomized Numerical alignEr), a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. ERNE comprises ERNE-FILTER (read trimming and continamination filtering), ERNE-MAP (core alignment tool/algorithm), ERNE-BS5 (bisulfite treated reads aligner), and ERNE-PMAP/ERNE-PBS5 (distributed versions of the aligners),

This project has been moved to https://github.com/draeger-lab/SBSCL.

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. Xmipp is a well-known package in the EM image processing. It is integrated...

GTdb - Modular genotype database for all markers. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.

The metabolomics standards initiative (msi) will develop a Core Information for Metabolomics Reporting (CIMR) recommendation and a more formal and semantically defined corresponding ontology (msi-ontology).

Frida is image analysis software. Frida was developed by the Johns Hopkins University Tissue Microarray Core Facility. It is open source and written in 100% Java. Frida makes use of functionality from the NIH's ImageJ application. Note: Frida was integr

STJUDE-SRM is a laboratory management system designed to support shared resource facility (or core lab) activities. It was designed and developed by the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital.

SeqTRACS is a Laboratory Information Management System for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. Trace files are tracked in a database and can be retrieved by users

HmmSDK is a hidden Markov model (HMM) software development kit written in Java. It consists of core library of HMM functions (Forward-backward, Viterbi, and Baum-Welch algorithms) and toolkits for application development.

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms).