Open Source Java Scientific/Engineering Software for Desktop Operating Systems

Download the full version at: https://www.sweethome3d.com/download.jsp?adid=sourceforge Sweet Home 3D is an interior design application that helps you to quickly draw the floor plan of your house, arrange furniture on it, and visit the results in 3D.

JDiskMark is a powerful and versatile disk benchmarking tool written in Java, designed to help measure the performance and health of your storage drives. Whether you're testing HDDs, SSDs, or network locations, JDiskMark provides reliable insights into your disk's read and write speeds. ubuntu: https://sourceforge.net/projects/jdiskmark/files/0.9.0/jdiskmark_0.9.0_amd64.deb/download rhel/fedora: https://sourceforge.net/projects/jdiskmark/files/0.9.0/jdiskmark-0.9.0-1.x86_64.rpm/download macos: https://sourceforge.net/projects/jdiskmark/files/0.9.0/jdiskmark-0.9.0.pkg/download windows: https://sourceforge.net/projects/jdiskmark/files/0.9.0/jdiskmark-0.9.0.msi/download ZIP releases require java to be installed separately: * 0.6.3-current > jdk25 * 0.5.0-0.6.2 >jdk21 * 0.1-0.4 > Jdk8

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 tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more!

BRL-CAD is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.

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/

The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments for bacterial and archaeal 16S rRNA sequences, fungal LSU and fungal ITS sequences, with confidence estimates for each assignment. More information and tutorials on how to install, use and retrain RDP Clasifier can be found on at https://github.com/rdpstaff/classifier and John Quensen's blog (https://john-quensen.com/). Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. 2. Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc. 2024 Apr 11;13(4):e0106323.

Cross-platform data acquisition and visualization software with an embedded HTTP-server, binary protocol parsing library, protocol emulation server, remote secure administration server, embedded Groovy scripting facilities and HMI (SCADA) visualization module.

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gVirtualXRay is a C++ library to simulate X-ray imaging. It is based on the Beer-Lambert law to compute the absorption of light (i.e. photons) by 3D objects (here polygon meshes). It is implemented on the graphics processing unit (GPU) using the OpenGL Shading Language (GLSL). SimpleGVXR is a smaller library build on the top of gVirtualXRay. It provides wrappers to Python, R, Ruby, Tcl, C#, Java, and GNU Octave.

PileWorks provides the organizational structure for coordinating several different projects which approach some aspect of Pile Technology. PileWorks defines a set of interfaces and implements some basic infrastructure for Pile engines and agents.

TXM is a free and open-source cross-platform Unicode & XML based text analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine (http://cwb.sourceforge.net) and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages (http://www.r-project.org). Read the scientific background at the Textométrie project web site http://textometrie.ens-lyon.fr/?lang=en. Read a full description at the TEI Tools wiki http://wiki.tei-c.org/index.php/TXM.

Impact is an explicit Finite Element Program Suite which simulates dynamic impact events. It has a range of elements, contact handling and different material laws. Models can be created, solved and analyzed with the included pre- and postprocessor. Impact is based on an Explicit Time stepping algorithm. These kind of codes are used to simulate dynamic phenomena such as car crashes and similar, usually involving large deformations.

The Avalon Cheminformatics Toolkit contains tools to render and canonicalize SMILES and manipulate MOL file and related formats as well as structure fingerprinting.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

Jitterbit is an open source integration tool that delivers a quick and simple way to design, configure, test, and deploy integration solutions. It supports many document types and protocols: XML, web services, database, LDAP, text, FTP, HTTP(S), file

ORT is a tool for modelling and flying launch vehicles of arbitrary size and complexity. Unlike OpenRocket, it does not focus on amateur rockets but on real-world launch vehicles. The bundle includes a graphical design tool with an integrated simulation engine for rocket launches. Also included in the bundle is a playback application and a headless driver for logging simulations into spreadsheets. ORT integrates JME3 for 3D rendering.

Fachwerk3D calculates three-dimensional strut-and-tie models used by structural engineers for analysing and designing reinforced concrete structures. The program only uses the equilibrium conditions, thus it is not assuming elastic behaviour.

Entrainer is a Java program (JRE 1.8.0_40+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.

The Rossum Project is an attempt to collect and distribute robotics software. We are seeking help with our first project, a mobile-robot simulator featuring a 2-D virtual world, and new work including artificial intelligence and robot-control logic.

Fachwerk calculates strut-and-tie models used by structural engineers for analysing and designing reinforced concrete structures. The program only uses the equilibrium conditions, thus it is not assuming elastic behaviour.

jATLAS is a Java implementation of ATLAS [Architecture and Tools for Linguistic Analysis Systems]. For more information, see http://jatlas.sourceforge.net.

A verilog language compiler written using Java and JavaCC. It produces a netlist, an ascii text file, of all the cell connections. It can compile very large circuits comprised of many modules.

You can download the Color Mod at the Biogenesis main site too (included in the main download now). You also find the sourcecode there. If you want to post a review, remember that this is only a modification, so comment on my changes, not on the simulation. Original project by Joan Queralt Molina: https://sourceforge.net/projects/biogenesis/ Includes Tyler Colemans "Features Mod": https://sourceforge.net/projects/biogenesisfeatu/ Biogenesis discussion forum: https://sourceforge.net/p/biogenesis/discussion/ Biogenesis runs faster (at least for myself) if you open a Google Chrome window (don´t know why :D)

A portable library to access braille displays.

Arezzo is an emulator of a Flexible Manufacturing System (FMS) usable with the "Bench4star" benchmark.