Open Source Java Data Analytics Tools for BSD

Software for pixelization, hierarchical indexation, synthesis, analysis, and visualization of data on the sphere. Please acknowledge HEALPix by quoting the web page http://healpix.sourceforge.net (or https://healpix.sourceforge.io) and publication: K.M. Gorski et al., 2005, Ap.J., 622, p.759 Full software documentation available at https://healpix.sourceforge.io/documentation.php Wiki Pages: https://sourceforge.net/p/healpix/wiki/Home Exchanging Data with HEALPix (in FITS files): https://sourceforge.net/p/healpix/wiki/Exchanging%20Data%20with%20HEALPix/ GDL and FL users should read https://sourceforge.net/p/healpix/wiki/HEALPix%20and%20GDL/

DataMelt (or "DMelt") is an environment for numeric computation, data analysis, computational statistics, and data visualization. This Java multiplatform program is integrated with several scripting languages such as Jython (Python), Groovy, JRuby, BeanShell. DMelt can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Neural networks and various data-manipulation methods are integrated using powerful Java API. Elements of symbolic computations using Octave/Matlab scripting are supported.

PMM-Lab is an open-source extension to the Konstanz Information Miner (KNIME). It consists of three components: • a library of KNIME nodes (called PMM-Lab), • a library of “standard” workflows • an HSQL database.to store experimental data and microbial models. Altogether these components are designed to ease and standardize the statistical analysis of experimental microbial data and the development of predictive microbial models (PMM). Users can apply PMM-Lab to proprietary or public data and create bacterial growth / survival / inactivation models. The framework can easily be extended to other model types, e.g. growth/no-growth boundary models. PMM-Lab has been initiated and provided by the Federal Institute for Risk Assessment - BfR (Berlin, Germany). The software is in Beta status. Before using the software you have to read and accept the license and disclaimer (https://sourceforge.net/p/pmmlab/wiki/Disclaimer/). If you do not agree, do not use this software.

The Integrated Analysis Platform (IAP) has been designed and developed to support the analysis of large-scale image data sets of different camera systems. It aims in bridging different data domains and in integrating different approaches to data analysis and post-processing.

BIRBU (BIological Relationship BUilder) is a Java tool for microarray gene expression data analysis. BIRBU identifies biologically significant relationship between genes using microarray data and prior knowledge on relationships between genes.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.

A framework for image analysis and data analysis, aimed towards microscopy and the needs of current research.

EDAS2 is a web-based environmental quality data management and decision support framework

EyeMap is a visualization and analysis tool for text reading eye movement data. It can process Unicode, proportion/non-proportion and spaced/unspaced reading materials, which supports various languages and experiment methods.

GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.

GmanDA is a GPL software for performing qualitative data analysis on mailing-lists and mboxes. It was developed to ease the work with large scale mailing-list archives taken from Gmane.org

JNeuron is an analysis tool for multi-neuronal spike train analysis. The tool will allow scientists to organize their spike train data analysis into projects. The tool will implement standard spike train analysis algorithms and also datamining algorithms

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.

Parallel Colt is a multithreaded version of Colt - a library for high performance scientific computing in Java. It contains efficient algorithms for data analysis, linear algebra, multi-dimensional arrays, Fourier transforms, statistics and histogramming

A shell for using the methods of Contextual Logic to do qualitative data analysis, mathematical research on the theory underlying Conceptual Knowledge Processing, or learning Formal Concept Analysis. It uses the framework provided by the Tockit project..

SCaVis is an environment for scientific computation, data analysis and data visualization for scientists, engineers and students. The program is fully multiplatform (100% Java) and integrated with Java and a number of scripting languages: Jython (Python), Groovy, JRuby, BeanShell. SCaVis can be used to plot functions and data in 2D and 3D, perform statistical tests, data mining, numeric computations, function minimization, linear algebra, solving systems of linear and differential equations. Linear, non-linear and symbolic regression are also available. Elements of symbolic computations using Octave/Matlab scripting are supported. The project was migrated to DataMelt.

A mini data CUBE to do some embedded data analysis and mining.

jHepWork (2005-2013) was an environment for scientific computation, data analysis and data visualization for scientists, engineers and students. The program is fully multiplatform (100% Java) and integrated with the Jython (Python) scripting language. Currently the project is known under the name DataMelt (https://datamelt.org)

Java OpenCL Process Virtual Machine. Spring IoC based framework for complex data analysis with OpenCL computing.

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.