Science software

The Experimental Physics and Industrial Control System (EPICS) is a software environment used to develop and implement distributed control systems to operate devices such as particle accelerators, telescopes and other large experiments.

SCIgen is a computer program that uses context-free grammar to randomly generate nonsense in the form of computer science research papers.

Marble is a virtual globe application which allows the user to choose among the Earth, the Moon, Venus, Mars and other planets to display as a 3-D model.

RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.

SciPy (pronounced "Sigh Pie") is an open source Python library used for scientific computing and technical computing.

NumPy (pronounced "Numb Pie" or sometimes "Numb pee") is an extension to the Python programming language, adding support for large, multi-dimensional arrays and matrices, along with a large library of high-level mathematical functions to operate on these arrays.

MathType is a software application created by Design Science that allows the creation of mathematical notation for inclusion in desktop and web applications.

Wolfram Mathematica (sometimes referred to as Mathematica) is a symbolic mathematical computation program, sometimes called a computer algebra program, used in many scientific, engineering, mathematical, and computing fields.

In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.

PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).

gretl is an open-source statistical package, mainly for econometrics.

matplotlib is a plotting library for the Python programming language and its numerical mathematics extension NumPy.

Presentation is a Windows software application for conducting psychological and neurobehavioral experiments, developed by Neurobehavioral Systems Inc.

UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

The Naval Observatory Vector Astrometry Software (NOVAS) is a software library for astrometry-related numerical computations.

NCSS is a statistics package produced and distributed by NCSS, LLC.

NEST is a simulation software for spiking neural network models, including large-scale neuronal networks.

Range Software is finite element analysis software package.

Plotly, also known by its URL, Plot.

MovAlyzeR is a software package for handwriting movement analysis for research and professional applications.

3D Virtual Creature Evolution, abbreviated to 3DVCE, is an artificial evolution simulation program created by Lee Graham.

Advanced Chemistry Development, Inc.

Amira (pronounce: Ah-meer-ah) is a software platform for 3D and 4D data visualization, processing, and analysis.

Avizo (pronounce: ‘a-VEE-zo’) is a general-purpose commercial software application for scientific and industrial data visualization and analysis.

PASS is a computer program for estimating sample size or determining the power of a statistical test or confidence interval.

PeakFit is an automated nonlinear peak separation and analysis software package for scientists performing spectroscopy, chromatography and electrophoresis.

FAMOS is a graphical data analysis program for evaluating and visually displaying measurement results.

AnimatLab is an open-source neuromechanical simulation tool that allows authors to easily build and test biomechanical models and the neural networks that control them to produce behaviors.

Bilbao Crystallographic Server is an open access website offering online crystallographic database and programs aimed at analyzing, calculating and visualizing problems of structural and mathematical crystallography, solid state physics and structural chemistry.

FORM is a symbolic manipulation system.

GraphPad InStat is a commercial scientific statistics software published by GraphPad Software, Inc.

The LONI Pipeline is a free distributed system for designing, executing, monitoring and sharing scientific workflows on grid computing architectures.

LabRAD (RAD = Rapid Application Development) is an open source data acquisition and instrument control platform targeted at (university) research laboratories.

OE-Cake, OE-CAKE! or OE Cake is a 2D fluid physics sandbox which was used to demonstrate the Octave Engine fluid physics simulator created by Prometech Software Inc.

SequenceL is a general purpose functional programming language and auto-parallelizing (Parallel computing) tool set, whose primary design objectives are performance on multi-core processor hardware, ease of programming, platform portability/optimization, and code clarity and readability.

Maxim DL is an astronomical software created by Cyanogen Imaging for the intended purpose of astronomical imaging.

Tinker, stylized as TINKER, is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers.

1000Minds is online decision-making software for ranking, prioritizing or choosing between alternatives in situations where a variety of objectives or criteria need to be considered simultaneously (i.e., multi-criteria decision making).

ILNumerics is a mathematical class library for Common Language Infrastructure (CLI) developers and a domain specific language (DSL) for the implementation of numerical algorithms on the .

tomviz is an open source software platform for reproducible volumetric visualization and data processing.

Analytica is a visual software package developed by Lumina Decision Systems for creating, analyzing and communicating quantitative decision models.

CNS or Crystallography and NMR system, is a software library for computational structural biology.

IMOD is an open-source, cross-platform suite of modeling, display and image processing programs used for 3D reconstruction and modeling of microscopy images with a special emphasis on electron microscopy data.

AKtoolbox is a Matlab toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) and has been developed independently of Matlab Bioinformatics Toolbox.

PicoScope is a computer software for real-time signal acquisition of Pico Technology oscilloscopes.

PhotoModeler is a software application that performs image-based modeling and close range stereophotogrammetry – producing 3D models and measurements from photography.

Pipeline Pilot is the authoring tool for the Accelrys Enterprise Platform.

MasterPlex QT is curve-fitting software published by the MiraiBio Group of Hitachi Software Engineering America, Ltd.

MathMagic is a mathematical WYSIWYG equation editor, available for Windows, Mac OS X, Android and iOS since its debut in 1998.

MeVisLab is a cross-platform application framework for medical image processing and scientific visualization.

Montage (full name Montage Astronomical Image Mosaic Engine) is a software toolkit used in astrophotography to assemble astronomical images in Flexible Image Transport System (FITS) format into composite images, called mosaics, that preserve the calibration and positional fidelity of the original input images.

MasterPlex ReaderFit is a commercial curve-fitting software designed specifically for elisa assay analysis published by the MiraiBio Group of Hitachi Solutions America, Ltd.

GraphPad Prism is a commercial scientific 2D graphing and statistics software published by GraphPad Software, Inc.

DataMelt (or, in short, DMelt) a computation and visualization environment, is an interactive framework for scientific computation, data analysis and data visualization designed for scientists, engineers and students.

MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language.

MountainsMap is a surface imaging and metrology software published by the company Digital Surf.

Orange is a free software machine learning and data mining package (written in Python).

CoNTub is a software project written in Java which runs on Windows, Mac OS X, Linux and Unix Operating systems through any Java-enabled web browser.

SOCET SET is a software application that performs functions related to photogrammetry.

Treefinder is a computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences.

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models.

DataScene is a scientific graphing, animation, data analysis, and real-time data monitoring software package.

In 1997 FEMA released its first edition of a commercial off-the-shelf loss and risk assessment software package built on GIS technology.

Insilicos is a life science software company founded in 2002 by Erik Nilsson, Brian Pratt and Bryan Prazen.

Integrated Software for Imagers and Spectrometers, also abbreviated to Isis, is a specialized software package developed by the USGS to process images and spectra collected by current and past NASA planetary missions sent to Earth's Moon, Mars, Jupiter, Saturn, and other solar system bodies.