Open Source Data Analytics Tools - Page 11

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).

Microarray Data Analysis System, a Java application, provides an intuitive graphical scripting interface to design analysis protocols and perform normalization and filtering to microarray data by a variety of implemented statistical analysis modules.

Software quality assurance is essential in genomic medicine. Nonetheless there is currently no systematic evaluation of existing computational tools used for whole genome or whole exome sequencing data analysis. We developed a Metamorphic Testing tool that tests three widely used short-read alignment programs (BWA, Bowtie and Bowtie2) in order to systematically evaluate their performance.

Data processing and analysis in proteomic studies is a significant challenge and very time consuming. MS Data Miner (MDM) is a freely available web-based software to analyze, process, validate, compare, and display output files from MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science) and ProteinPilot (AB Sciex). It was developed to significantly decrease the data analysis time and to handle large proteomic studies. This open sourced system includes a spectra validation-system and automatically screenshot generation tool for Mascot-assigned spectra. In addition, a GO term analysis function and a tool for generating comparative data-reports are included. The software is described in the following paper: Dyrlund TF, Poulsen ET, Scavenius C, Sanggaard KW, Enghild JJ. MS Data Miner: A web-based software tool to analyze, compare and share mass spectrometry protein identifications. PROTEOMICS 2012 http://www.ncbi.nlm.nih.gov/pubmed/22833312

Advances in high-resolution mass spectrometry facilitate the identification of hundreds of metabolites, thousands of proteins and their post-translational modifications. This remarkable progress poses a challenge to data analysis and visualization, requiring methods to reduce dimensionality and represent the data in a compact way. To provide a more holistic view, we recently introduced circular proteome maps (CPMs). However, the CPM construction requires prior data transformation and extensive knowledge of the Perl-based tool, Circos. We present MS-Helios, an easy to use command line tool with multiple built-in data processing functions, allowing non-expert users to construct CPMs or in general terms circular plots with a non-genomic basis. MS-Helios automatically generates data and configuration files to create high quality and publishable circular plots with Circos.

Mass spectrometer is a useful tool for biochemistry research field analysis. It is used to identify microorganisms, protein, chemical compounds and complex diseases by blood analysis. There is many tools and libraries to handle different steps of mass spectrometry (MS) data analysis. However, the integration of all these tools lacks user friendly approaches. We developed a machine learning solution capable to handle all steps of MS data analysis. The ML-MS Tool is an free software that integrate different mass spectrometry analysis techniques with machine learning approach. We focused in automatic feature extraction, avoiding the need of manual peaks analysis of biomarkers. With all feature extracted ML-MS versatile classification tool avoiding the need reprocess the new MS samples. ML-MS is divided into two sub-products, the ML-MS Tool and the ML-MS Library; both products are free and open source. The ML-MS Library is focused on script routines.

A user-friendly lightweight BI tool. It is a set of plugins of MTTK Lowcode Engine, so the user manual and develop manual are combined together with MTTK Low Code Engine. Code repository: https://github.com/jamie-mttk/mttk-lowcode-designer Online demo available at http://139.129.210.30:8825 (First visit may be slow) Username: admin Password: 123456 Lightweight No data processing engine offered, all the data processing depends on the target Databse Server. Easy to use For example ,to build an echart need to provide many many configurtaions/options, such as title location, grid position,etc. To simplified the usage ,only the important options should be configured by user with default setting, other options are set by BI system automatically.

LMS Tools is a set of tools and libraries for administrators and users of learning management systems to perform, for example, portal integration, LMS management or usage data analysis.

MathROOT is a tool for high-energy physicists to access the ROOT data analysis framework from within Mathematica

A set of Matlab functions which compute effect size statistics and (exact) confidence intervals for a wide range of data analysis situations, including two-sample-, oneway-, twoway- and contrast analyses as well as categorical data in tables.

An end-to-end solution for medical management including dispatching medical units, employee management, medical billing, and data analysis.

A tool to support data-analysis on a Oracle-DB. In Greek mythology, Metis (Μῆτις) was of the Titan generation ... The Stoic commentators allegorized Metis as the embodiment of "wisdom" or "wise counsel" ... (from Wikipadia)

Microarray data analysis tool for detection of chromosomal abberations, statistical evalutation of evidence and visualization of expression levels.

A MATLAB-based software package for microbiological research designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

MoDAVE aims at providing data analysis and visualization extensions to Mosaic datasets, including cubed sphere data, to the Climate Data Analysis Tools (CDATA) in particular.

ModuleFair is a generic, module-based framework upon which to quickly build anything from data analysis programs to game level editors. This project is no longer maintained.

MolBioLib is a compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. MolBioLib is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. While MolBioLib was designed primarily for bioinformatics purposes, much of its functionality is applicable to a wide range of problems. Complete documentation and an extensive automated test suite are provided. This package assumes fluency in both UNIX and C++.

Mundo-Bioq permit to collect patient data, analysis data, and accounting of laboratory data. It's focused to small laboratories that speak spanish. It's developed in FoxPro/DOS and run in in DOS, but also can run in Linux (under DOSEMU), and any Win

NLOPredict is a nonlinear optical prediction and data analysis tool. Nonlinear optical measurements can yield information about the structure of crystals, and orientation of molecules at surfaces and interfaces.

This project is aimed at being able to log information from a NMEA gps in the back ground for later data analysis. It also has the ability to convert the raw log data into a Google Earth KML file for viewing.

Comprehensive device automation and data analysis framework

Open Source Development of (SmartGrid) Data Analysis Platform based on OpenPDC and Cloud Computing Technology. * Source Codes - http://nephee.sourceforge.net, Main Project (Info, Planning, News) , http://nephee.or.kr, http://twitter.com/nepheer

Novel Insight Scoring is analytical CRM software for automatically scoring customers given example (scored) data. The user of the software can set optimization time and adjust risk level (pessimistic, neutral or optimistic scoring) and score new customers without detailed knowledge about data analysis and machine learning methods. The scoring results are stored in a CSV file for further processing and importing to databases etc.