Showing 4992 open source projects for "research"

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  • 1

    BBMap

    BBMap short read aligner, and other bioinformatic tools.

    This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and...
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    Downloads: 292 This Week
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  • 2
    MEKA

    MEKA

    A Multi-label Extension to Weka

    Multi-label classifiers and evaluation procedures using the Weka machine learning framework.
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    Downloads: 36 This Week
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  • 3
    winPenPack

    winPenPack

    The portable software collection

    winPenPack is a project that aims at collecting the most frequently used and most popular open source applications made portable, so that they can be executed without installation from any USB Flash Drive or Hard Disk. The winPenPack suites offer a wide range of portable applications like office tools, internet tools, multimedia tools, development tools, security applications and other frequently used utilities. Everything you need, completely free, open source and portable!
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    Downloads: 294 This Week
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  • 4
    BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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    Downloads: 124 This Week
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    FrostWire

    FrostWire

    Search, Download, Play, Share on Bittorrent and the cloud

    FrostWire https://www.frostwire.com/ is a media player, Video Downloader and Peer to Peer (P2P) information sharing client for the BitTorrent network. This project is not affiliated with LimeWire LLC. FrostWires' source code is Licensed under the GNU GPL and Apache Open Source licenses. System Requirements Any of the following operating systems: ● Windows 10, 8, 7, Vista for Intel processors (64-bit only) ● Mac OS X 10.11 (El Capitan) or later (64-bit) ● Linux, Unix...
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    Downloads: 269 This Week
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  • 6
    CERCA

    CERCA

    CERCA – Citation Extraction & Reference Checking Assistant

    CERCA is an open-source research tool that supports the verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports. It is intended for: - Researchers performing final manuscript checks - Reviewers assessing reference consistency - Editors supporting editorial quality control - Meta-research and reproducibility workflows CERCA is an experimental tool. ...
    Downloads: 6 This Week
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  • 7
    Groove
    NOTE: The GROOVE codebase has moved to https://github.com/nl-utwente-groove
    Downloads: 20 This Week
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  • 8
    GeoTools, the Java GIS toolkit

    GeoTools, the Java GIS toolkit

    Toolkit for working with and mapping geospatial data

    GeoTools is an open source (LGPL) Java code library which provides standards compliant methods for the manipulation of geospatial data. GeoTools is an Open Source Geospatial Foundation project. The GeoTools library data structures are based on Open Geospatial Consortium (OGC) specifications.
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    Downloads: 498 This Week
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  • 9
    Community Z Tools

    Community Z Tools

    Tool support for the Z formal notation

    Community Z Tools Project (CZT): Tools for editing, typechecking and animating Z specifications and related notations. Includes a Java framework for building formal methods tools. NOTE: development of CZT has now moved to GitHub: https://github.com/community-z-users/czt
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    Downloads: 45 This Week
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  • 10
    AtomicJ

    AtomicJ

    Application for analysis of AFM data

    AtomicJ is an application for analysis of force microscopy recordings, including images and force curves. It allows for fast and reliable processing of single force curves and force maps, providing estimation of the mechanical properties of the sample. AtomicJ supports a wide range of contact mechanics models, including the models for blunt tips, the corrections for the effect of finite sample thickness, models of adhesive contact and models of spherical indentation of hyperelastic...
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    Downloads: 24 This Week
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  • 11
    GeoWebCache

    GeoWebCache

    GWC is a tile server and caching proxy written in Java

    GeoWebCache is a WMS tile cache that lets you serve cached map data to WMS clients, Goole Earth, Google Maps and MS Virtual Earth. The system is pluggable on both ends and does automatic matching to the best available tile. It is very fast and scalable.
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    Downloads: 43 This Week
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  • 12
    Jmol

    Jmol

    An interactive viewer for three-dimensional chemical structures.

    Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other...
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    Downloads: 606 This Week
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  • 13
    JGraphT
    JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. JGraphT supports a rich gallery of graphs and is designed to be powerful, extensible, and easy to use.
    Downloads: 25 This Week
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  • 14
    Advanced Trigonometry Calculator

    Advanced Trigonometry Calculator

    Open-source C/C++ math engine for advanced scientific computing

    Advanced Trigonometry Calculator (ATC) is an open-source mathematical computing engine written mainly in C/C++. Created in 2011 and maintained by Renato Alexandre dos Santos Freitas, ATC is designed as a practical Windows desktop application for advanced calculations, automation, and technical problem solving. ATC supports equation solving, polynomial tools, complex numbers, matrix calculations, statistics, physics, geometry, unit conversions, DSP/FFT operations, and scripting. It can...
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    Downloads: 161 This Week
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  • 15
    Hypernomicon

    Hypernomicon

    Hypertext-infused philosophy personal database software

    Hypernomicon is a personal productivity/database application for researchers that combines structured note-taking, mind-mapping, management of files (e.g., PDFs) and folders, and reference management into an integrated environment that organizes all of the above into semantic networks or hierarchies in terms of debates, positions, arguments, labels, terminology/concepts, and user-defined keywords by means of database relations and automatically generated hyperlinks (hence ‘Hyper’ in the...
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    Downloads: 22 This Week
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  • 16
    Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format
    Downloads: 26 This Week
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  • 17
    JaCoP
    JaCoP is a Java Constraint Programming solver. It provides a significant number of (global) constraints to facilitate efficient modeling of combinatorial problems, as well as modular design of search. Documentation is available at project Web site. Please, note that the sources from version 4.0 are only available at GitHub.
    Downloads: 3 This Week
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  • 18
    Eclipse 4diac

    Eclipse 4diac

    Eclipse 4diac the open source solution for industrial automation

    Eclipse 4diac is an open source PLC environment allowing to implement industrial control solutions in a vendor neutral way. 4diac implements IEC 61499 extending IEC 61131-3 with improved support for controller to controller communication and dynamic reconfiguration. With that 4diac provides the infrastructure for Industrie 4.0 and industrial IoT. Further information and the latest versions can be found here: https://eclipse.dev/4diac/
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    Downloads: 41 This Week
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  • 19
    Dynamic geometry program for use in schools and universities. Rich graphical interface, web export, graphics export, macros, assignments, animations and much more. Download the program via the links on the web page.
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    Downloads: 27 This Week
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  • 20
    JaxoDraw

    JaxoDraw

    JaxoDraw: Feynman Diagrams made easy!

    JaxoDraw is a tool to generate Feynman diagrams in a mouse click-and-drag fashion. Graphs can be exported to a variety of graphics formats and arbitrary latex code can be used for labels to produce high-quality publishing-style figures.
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    Downloads: 47 This Week
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  • 21
    Grassroots DICOM

    Grassroots DICOM

    Cross-platform DICOM implementation

    Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP. It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE and deflated transfer syntax. It comes with a super fast scanner implementation to quickly scan hundreds of DICOM files. It supports SCU network operations (C-ECHO, C-FIND, C-STORE, C-MOVE). PS 3.3 & 3.6 are distributed as XML files. It also provides PS 3.15 certificates and password based mecanism to anonymize and de-identify DICOM datasets.
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    Downloads: 90 This Week
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  • 22
    The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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    Downloads: 47 This Week
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  • 23
    Downloads: 7 This Week
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  • 24
    Local-search based solver of Constraint Satisfaction and Optimization Problems.
    Downloads: 4 This Week
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  • 25
    The Chemistry Development Kit
    The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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    Downloads: 28 This Week
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