Open Source BSD Scientific/Engineering Software

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 quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

PSRCHIVE is an application suite and development library for use in the storage and analysis of pulsar astronomical data. It includes an extensive range of algorithms and tools commonly used in a wide variety of experiments.

OpenJUMP is a community driven fork of JUMP the "Java Unified Mapping Platform" GIS software. The original JUMP was developed by Vivid Solutions, released under GPL2 in 2003 and discontinued in 2006. During 2004 already some enthusiastic developers joined together to enhance further the features of JUMP. They launched an independent development branch called OpenJUMP. The name gives credit to the original JUMP development, and at the same time describes the objectives of this project to be fully open to anyone wanting to contribute. These days OpenJUMP is developed and maintained by (some few) volunteers around the globe. If you need functionality or even better want to contribute you are very welcome to contact us at our mailing list.

SOFA is a statistics, analysis, and reporting program with an emphasis on ease of use, learn as you go, and beautiful output.

Line-drawing and polygon-filling rasterization algorithms in Java. Simple 2D package and more complex 3D package with Z-buffering. Texture mapping not supported at the moment. Color interpolation for lines, Gouraud shading for polygons fully supported. Floating point vertex coordinates, not integer. Pixel-level aliasing, not endpoint aliasing. Doesn't use Bresenham line style! Works with all Java versions. No external dependencies. Suitable for study in academic institutions, especially as related to line-drawing accuracy. Particular attention to detail concerning chopping of accumulation errors, using a cast from 64 bit to 32 bit strategy, in the interval [1.0,2.0). Individual pixel errors with overlapping polygons or line segments are about one in a billion, but I can't reproduce any errors at the moment by using random number generation with tens of millions of cases. Emphasis not only on correctness, but also on performance for real-world use or hardware implementation.

gretl is a cross-platform software package for econometric analysis, written in the C programming language.

GPS log file viewer and analyzer with support for GPX, TCX, KML, FIT, IGC, NMEA, SLF, SML, LOC, GPI, GeoJSON and OziExplorer files.

The high performance open source package for statistical data analysis StatAnt is a standalone cross-platform application. Completely free. No donation required. StatAnt comes with absolutely no warranty.

SaVi - simulate Starlink, Iridium, Globalstar, O3b, GPS, Galileo and other satellite constellations, modify them, or design your own. Requires Tcl/Tk and Unix libraries; 3D viewing option requires Geomview running on X Window.

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

GCBASIC is an open-source BASIC compiler for 8 bit Microchip PIC, Atmel AVR legacy, AVRDx and LGT microcontrollers. Also included in the project is Graphical GCBASIC, an icon based editor for GCBASIC programs. This is a continuous release project. The latest release is always available. This will give you the most complete development toolchain to create and program 8-bit PIC, AVR and LGT microcontrollers. We have added new capabilities that make GCBASIC the easiest tool set available - supporting over 1300's microcontrollers with tools to make this fun and simple. Please see the download section for your options. We have two IDEs, we have just the compiler and we have a minimal install - it is your choice. Please see the homepage here: http://gcbasic.sourceforge.net and also see http://gcbasic.sourceforge.net/download.html for other GCBASIC download options.

A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis.

dcm4che is an implementation of DICOM and IHE actors in Java. Homepage: http://www.dcm4che.org, Google Group: http://groups.google.com/group/dcm4che?hl=en, Wiki: http://www.dcm4che.org/confluence, Issue Tracking: http://www.dcm4che.org/jira

Android, Symbian UIQ 3.0 and Symbian Series 60 Edition 5 open-source software, tools, libraries and themes. Most notable the FX-602P / FX-603P Simulator and the HP-45 Emulator are hosted here.

Agena is an easy-to-learn procedural programming language suited to be used in scientific, mathematical, scripting, networking, and many other applications. Binaries are available for Solaris, Windows, Linux, OS/2, Mac OS X, Raspberry Pi and DOS.

The goal of this project is to open the OpenFOAM CFD toolbox to community contributed extensions. Visit https://sourceforge.net/p/openfoam-extend/wiki/Home/ for more information. OPENFOAM(R) is a registered trademark of OpenCFD Limited.

Maxima is a computer algebra system comparable to commercial systems like Mathematica and Maple. It emphasizes symbolic mathematical computation: algebra, trigonometry, calculus, and much more. For example, Maxima solves x^2-r*x-s^2-r*s=0 giving the symbolic results [x=r+s, x=-s]. Maxima can calculate with exact integers and fractions, native floating-point and high-precision big floats. Maxima has user-friendly front-ends, an on-line manual, plotting commands, and numerical libraries. Users can write programs in its native programming language, and many have contributed useful packages in a variety of areas over the decades. Maxima is GPL-licensed and largely written in Common Lisp. Executables can be downloaded for Windows, Mac, Linux, and Android; source code is also available. An active community maintains and extends the system. Maxima is widely used. Additional add-on packages for Maxima can be found at: https://github.com/maxima-project-on-github/maxima-packages

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 Python2, Python3, R, Ruby, Tcl, C#, Java, and GNU Octave.

SAGA - System for Automated Geoscientific Analyses - is a Geographic Information System (GIS) software with immense capabilities for geodata processing and analysis. SAGA is programmed in the object oriented C++ language and supports the implementation of new functions with a very effective Application Programming Interface (API). Functions are organised as modules in framework independent Module Libraries and can be accessed via SAGA’s Graphical User Interface (GUI) or various scripting environments (shell scripts, Python, R, ...). Please provide the following reference in your work if you are using SAGA: Conrad, O., Bechtel, B., Bock, M., Dietrich, H., Fischer, E., Gerlitz, L., Wehberg, J., Wichmann, V., and Boehner, J. (2015): System for Automated Geoscientific Analyses (SAGA) v. 2.1.4. Geosci. Model Dev., 8, 1991-2007, https://doi.org/10.5194/gmd-8-1991-2015. For more information visit the project homepage and the wiki.

This is an official mirror of FreeCAD. Code and release files are primarily hosted on https://github.com/FreeCAD/FreeCAD and mirrored here. FreeCAD is a general purpose feature-based, parametric 3D modeler for CAD, MCAD, CAx, CAE and PLM, aimed directly at mechanical engineering and product design but also fits a wider range of uses in engineering, such as architecture or other engineering specialties. It is 100% Open Source and extremely modular, allowing for very advanced extension and customization. FreeCAD is based on OpenCasCade, a powerful geometry kernel, features an Open Inventor-compliant 3D scene representation model provided by the Coin 3D library, and a broad Python API. The interface is built with Qt. FreeCAD runs exactly the same way on Windows, Mac OSX and Linux platforms.

An extensive and multi-platform visualisation, process control and HMI application that supports many different devices via an open plug-in interface. Beside a visual GUI editor a debugger is part of the package.

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.

SLEEF stands for SIMD Library for Evaluating Elementary Functions. SLEEF implements vectorized versions of all C99 math functions, that utilize SIMD instructions of modern processors to make computation more efficient. The library also includes vectorized DFT subroutines.

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!

The high performance open source package for statistical data analysis Criterial is an add-in for all desktop versions of the LibreOffice Calc spreadsheets on any 64bit operating systems (UNIX, Linux, Windows). The combination of the unsurpassed convenience of spreadsheets as frontend and the maximum speed of the C programming language as backend. Contains user experience and the best ideas of projects AtteStat and StatAnt. Completely free. No donation required. Criterial comes with absolutely no warranty.