Fast C++ matrix library with easy to use functions and syntax, deliberately similar to Matlab. Uses template meta-programming techniques. Also provides efficient wrappers for LAPACK, BLAS and ATLAS libraries, including high-performance versions such as OpenBLAS and Intel MKL. Useful for machine learning, pattern recognition, signal processing, bioinformatics, statistics, finance, etc. For more details, see http://arma.sourceforge.net
OpenGTS (Open Source GPS Tracking System) is a full featured web-based GPS tracking system for your fleet of vehicles. It supports OpenLayers and other map providers, detail/summary Reporting, and various GPS tracking devices.
General Mission Analysis Tool
Do you want to go to Mars but don't know when to leave or how much to bring? Do you want to study Earth protection by planning a mission to a near-Earth asteroid? The General Mission Analysis Tool (GMAT) is an open-source space mission design tool to help you answer these and many other space flight challenges. GMAT is developed by a team of NASA, private industry, and public and private contributors. The GMAT development team is pleased to announce the release of GMAT version R2017a. For a complete list of new features, compatibility changes, and bug fixes, see the Release Notes. Below are just some of the new capabilities contained in this release. • New navigation data types • Preliminary Kalman filter • STK ephemeris propagation • Utility for managing data files (EOP etc.) • Collocation library • Preliminary API interface • Second level editing of navigation data
ECG Toolkit support for: SCP-ECG, DICOM, HL7 aECG, ISHNE & MUSE-XML
C# ECG Toolkit is an open source software toolkit to convert, view and print electrocardiograms. The toolkit is developed using C# .NET 2.0 (code also supports 1.1, 3.5 and 4.0). Support for ECG formats: SCP-ECG, DICOM, HL7 aECG, ISHNE and MUSE-XML.
World's first open source data quality & data preparation project
This project is dedicated to open source data quality and data preparation solutions. Data Quality includes profiling, filtering, governance, similarity check, data enrichment alteration, real time alerting, basket analysis, bubble chart Warehouse validation, single customer view etc. defined by Strategy. This tool is developing high performance integrated data management platform which will seamlessly do Data Integration, Data Profiling, Data Quality, Data Preparation, Dummy Data Creation, Meta Data Discovery, Anomaly Discovery, Data Cleansing, Reporting and Analytic. It also had Hadoop ( Big data ) support to move files to/from Hadoop Grid, Create, Load and Profile Hive Tables. This project is also known as "Aggregate Profiler" Resful API for this project is getting built as (Beta Version) https://sourceforge.net/projects/restful-api-for-osdq/ apache spark based data quality is getting built at https://sourceforge.net/projects/apache-spark-osdq/
Geoportal Server is a standards-based, open source product that enables discovery and use of geospatial resources including data and services.
Moved to https://github.com/rdiankov/openrave An open-source, cross-platform, plugin-based robot planning environment for autonomous robotics. Includes services like collision detection, physics, (inverse) kinematics, sensors, robot controls, python bindings, and a network scripting environment.
An Academic Literature Suite
Docear (pronounced dog-ear) is what we call an “academic literature suite”. It integrates everything you need to search, organize and create academic literature in a single application: a digital library, reference manager, PDF and file manager, note taking and mind mapping. And the best: Docear works seemlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader. Docear is free and open source, based on Freeplane, funded by the German Federal Ministry of Technology and developed by scientists from around the world, among others from OvGU, and the University of California, Berkeley.
Linking Language to Knowledge with Distributional Semantics
JobimText is a software solution for automatic text expansion using contextualized distributional similarity. It provides text analysis tools for large corpora and has capabilities to create distributional semantic models (JoBimText models) and multi-word expressions.
Comet open source tandem mass spectrometry (MS/MS) search engine.
Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, and ms2 files. Supported output formats are .out, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net
Massively parallel software for quantum chemistry calculations
Scalable Molecular Analysis Solver for High-performance computing systems (SMASH) is open-source software for massively parallel quantum chemistry calculations. It is currently capable of energy, analytical gradient, and geometry optimization calculations of Hartree-Fock theory and Density Functional Theory (DFT), and energy calculations of Second-order Moller-Plesset (MP2) perturbation theory. DFT calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
Java Disk Benchmark Utility
Simple Java utility to help bench mark disk IO. Benchmark is done by creating and reading data files to a user directory that can be configured. Suggestions would be very appreciated. https://gitlab.com/jamesmarkchan/jDiskMark/ Note: When doing a combined read and write operation the disk cache is not cleared automatically so the app must be restarted to avoid the cache from affecting read IO performance.
Libraries and command line tools for medical image processing.
This software provides libraries and command line tools for the processing and analysis of gray scale medical images.
a parallel short-read error corrector for Illumina sequencing
Musket is an efficient multistage k-mer based corrector for Illumina short read data. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage workflow. Our performance evaluation results, in terms of correction quality and de novo genome assembly measures, reveal that Musket is consistently one of the top performing substitution-error-based correctors. In addition, Musket is multi-threaded using a master-slave model and demonstrates superior parallel scalability compared to all other evaluated correctors as well as a highly competitive overall execution time.
Engineering structural analysis app for education
This specialist engineering app is designed as an educational tool for university students - but also has practical applications for anyone in structural engineering. A video tutorial guides you through the full functionality of this app which, once downloaded, forms a self-contained package packed with useful engineering applications. Wherever you are - even out in the field - LUCID/mercury lets you explore and analyse an array of structural engineering problems. At its core is the ability to import, view, edit solve and post-process simple models. These models are either pre-designed or you can even import your own based on industry standard file formats. You can also create a layout fior a structure based on a preliminary design, as well as performing section property calculations and laminate stuiffness analaysis - all with visual and data outputs. Able to read industry standard NASTRAN files, the app benefits from powerful graphics which allow you to fully rotate and enlarg
One of the leading short-/long-read aligner to large genomes
CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads.
Applications for data management
"Information is data in action", and, consequently, having good quality data is essential. The AESTEL package contains two highly configurable applications for data management: A data loader and a reporting application, i.e. DataLoader and AEREA, respectively. The data loader application applies user-defined instructions to validate, process and load data. The reporting application provides a query builder and spreadsheet template designer. Both applications work with any relational data model. (Postgres and Oracle have been tested). The two applications have been initially developed for small molecule drug discovery research. However, they can be extended for use in other data domains.
Symja - Java Computer Algebra System
Java Computer Algebra System. Features: math expression parser and evaluating API (jsr223), pattern matching. Moved to http://bitbucket.org/axelclk/symja_android_library
The software annotates text with 41 broad semantic categories (Wordnet supersenses) for both nouns and verbs; i.e., it performs both sense disambiguation and named-entity recognition. The tagger implements a discriminatively-trained Hidden Markov Model.
lightweight GPU-based sparse matrix-vector multiplication (SpMV)
LightSpMV is a novel CUDA-compatible sparse matrix-vector multiplication (SpMv) algorithm using the standard compressed sparse row (CSR) storage format. We have evaluated LightSpMV using various sparse matrices and further compared it to the CSR-based SpMV subprograms in the state-of-the-art CUSP and cuSPARSE. Performance evaluation reveals that on a single Tesla K40c GPU, LightSpMV is superior to both CUSP and cuSPARSE, with a speedup of up to 2.60 and 2.63 over CUSP, and up to 1.93 and 1.79 over cuSPARSE for single and double precision, respectively.
CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads with high error rates.
A platform for modelling influenza-like epidemics and containment
The Global Epidemic Simulator is a platform for modelling directly transmissible human diseases such as influenza, and testing intervention policies that may reduce the duration or severity of an outbreak of such a disease. Building on previous work, this model is spatial and individual-based, using various geographical and demographic data sources to place households at absolute locations, populated with individuals of specific ages who each attend schools or workplaces situated in their vicinity. The significant advance of this project over previous work is the global nature of simulation, the memory and performance requirements of which motivate us towards a multi-core, multi-computer solution.
Now part of Apache's Mahout machine learning project at http://mahout.apache.org/-- please see there for latest info and code and releases and support!
NAIL is a toolset for network analysis in the life sciences
The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results. These methods are designed as self-contained platform-independent components which can be called either from another program, or from a command line. Modelling biological systems as networks (graphs) is becoming a common approach in the life sciences. However, different algorithms typically use different input and output data types, are implemented using different technologies, and are demonstrated by application to different biological problems. Because of this, the primary goal of the NAIL project is to provide a straightforward way to use network approaches in the life sciences, and to apply a variety of techniques quickly and easily on the same data.
Mobile Web Server is a portable HTTP Server. No Installation Required ! You can use it from any Folder, USB Key (Flash Drive) or CDROM (Read Only).