Open Source Linux Data Analytics Tools

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 repository has been moved to: https://github.com/wojdyr/fityk. Fityk is nonlinear curve-fitting and data analysis software. It is specialized in fitting peaks (bell-shaped functions like Gaussian, Loretzian, Pearson7, Voigt) to experimental data.

HCS Analyzer is an open source software dedicated to High Content Screening data processing and analysis.

GRAIL Real Time Location Service (RTLS)

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.

PAScual is a data analysis suite for Positron Annihilation Lifetime Spectroscopy (PALS).

Set of tools for basic analysis of electrophysiological data. The Python classes show how to call OpenElectrophy functions and save data. The R library applies circular statistics to spike phase data and saves the best von Mises fit and the Rayleigh statistics on the disk. The wavelet coherence analysis is done in R by the package "sowas". Check the module R_coherence to see how we solved that problem. This packages may be useful for people who start using OpenElectrophy and circular statistics in R. If you find errors, please report them. The project is still in development, so in the future you'll get updates.

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.

PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this address: https://plateeditor.sourceforge.io - The source code is also available on GitHub, visit: https://github.com/vindelorme/PlateEditor More information about the source code and the API are available there (the wiki is still under construction, thanks for your patience!) For a list of recent updates, visit: https://sourceforge.net/p/plateeditor/wiki/Updates/ Hoping PlateEditor will make your life easier in the lab! If yes, please cite us: https://doi.org/10.1371/journal.pone.0252488

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.

CNV-WebStore is an integrated platform to analyse, store, visualise and interpret CopyNumber Variation data. Analysis is supported for Illumina data, all CNV-reports and raw data can be imported after third-party analysis. Contact system admin at http://cnv-webstore.uantwerpen.be for installation scripts

EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules.

Electron diffraction code for the simulation and data analysis of keV electron-molecule scattering.

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

GEDAS is a software to perform microarray data analysis with friendly user interface and convenient data display. Currently some commonly used data clustering algorithms have been implemented in this software.

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

HadStat is service on the cloud, allow you to analysis the data on the cloud and return the result in nice graph,this service is free, you can redistribute it and/or modify it under the terms of the GNU General Public License. this service using many technologies , like Hadoop mapreduce, HTML, PHP, Web Service applications, linux server, java, eclipse IDE, with many indicators:Simple moving average (SMA),Exponential moving average (EMA),Smoothed simple moving average (SMMA),Linear weighted moving average (LWMA )on DATA from NYSE daily prices.....

HyPhy is a comprehensive environment for maximum likelihood statistical analysis of genetic sequence data. It includes a large collection of out of the box analyses, a feature-rich graphical user interface for custom data analysis and a scripting languag

The hsdar package contains classes and functions to manage, analyse and simulate hyperspectral data. These might be either spectrometer measurements or hyperspectral images through the interface of rgdal.

Matlab freeware for data analysis, by J. M. Lilly

JProGraM (PRObabilistic GRAphical Models in Java) is a statistical machine learning library. It supports statistical modeling and data analysis along three main directions: (1) probabilistic graphical models (Bayesian networks, Markov random fields, dependency networks, hybrid random fields); (2) parametric, semiparametric, and nonparametric density estimation (Gaussian models, nonparanormal estimators, Parzen windows, Nadaraya-Watson estimator); (3) generative models for random networks (small-world, scale-free, exponential random graphs, Fiedler random fields), subgraph sampling algorithms (random walk, snowball, etc.), and spectral decomposition.

LaCor is intended for physical data analysis in High Energy Physics field. It was originally designed to aid in lambda hyperon correlations research in the Selex@FNAL experiment, but it should be useful for similar studies.

Larch is a scientific data processing language that is designed to be easy to use for novices and complete enough for advanced data processing and analysis. Larch provides a wide range of functionality for dealing with arrays of scientific data, and basic tools to make it easy to use and organize complex data. Larch has been primarily developed for dealing with x-ray spectroscopic and scattering data, especially the kind of data collected at modern synchrotrons and x-ray sources. Larch is written in Python and relies heavily on the standard tools for scientific computing with Python (numpy, scipy, matplotlib, and h5py).

Latest Code in GitHub: https://github.com/aquaskyline/MICA-aligner To better utilize MIC-enabled computers for NGS data analysis, we developed a new short-read aligner MICA that is optimized in view of MIC’s limitation and the extra parallelism inside each MIC core. Experiments on aligning 150bp paired-end reads show that MICA using one MIC board is ~4.85 times faster than the CPU-(multi-core)-based BWA-MEM and about the same speed as the GPU-based SOAP3-dp. Furthermore, MICA’s simplicity allows very efficient scale-up when multiple MIC boards are used in a node (3 cards gives a 14-fold speedup over 6-core BWA-MEM).