Science

Note: For possibly more up to date selection of scientific applications, try checking the

Mathematics

Calculator

See also .

Console

• — Arbitrary precision calculator language.

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• calc — Arbitrary precision console calculator.

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• clac — Command-line, stack-based calculator with postfix notation.

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• kalker — Command-line calculator with math syntax that supports user-defined variables and functions, complex numbers, and estimation of derivatives and integrals.

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• qalc — Command-line calculator and equation solver with fault-tolerant parsing, constant recognition and units.

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Graphical

• Deepin Calculator — Easy to use calculator for Deepin desktop.

• Extcalc — Qt-based scientific graphical calculator.

• FOX Calculator — Simple desktop calculator.

• galculator — GTK-based scientific calculator.

• Liri Calculator — Calculator for Liri.

• MATE Calc — Calculator for the MATE desktop environment.

• Qalculate! — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.

• SpeedCrunch — Fast, high precision and powerful cross-platform calculator.

Computer algebra system

• Maple — Famous commercial CAS. Often used in education.

• Mathics — A free CAS for symbolic mathematical computations which uses Python as its main language. It aims at achieving a Mathematica-compatible syntax and functions. It relies mostly on Sympy for most mathematical tasks and, optionally, Sage for more advanced functionality.

• wxMaxima — Graphical user interface for Maxima being a powerful computer algebra system.

Visualization of networks/graphs

• Graphviz — The established tool for displaying smallish graphs in 2D.

Scientific or technical computing

• EngLab — Cross-compile mathematical platform with a C like syntax.

• Octave — MATLAB-like language and interface for numerical computations.

• SageMath — Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.

Statistics

• R — Software environment for statistical computing and graphics.

Data analysis and plotting

• DataWarrior — Open-source data visualization and analysis program with embedded chemical intelligence.

• Engauge Digitizer — Extracts data points from images of graphs.

• Plots — A graph plotting application for GNOME.

See also List of applications/Documents#Spreadsheets.

Proof assistants

• Lean Theorem Prover — Proof assistant developed principally by Leonardo de Moura at Microsoft Research, used in conjunction with the Lean mathematical library.

Physics

Physics simulation

• Code_Aster — Software package for Civil and Structural Engineering finite element analysis (FEA) and numeric simulation in structural mechanics.

• Netgen/NGSolve — A high performance multiphysics finite element software, with a flexible Python interface to implement new physical equations and solution algorithms easily.

Unit conversion

• ConvertAll — Unit conversion application that allows one to combine units in any way (e.g. inches per decade), even if it does not make sense.

• Gonvert — Conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.

Chemistry

Molecules

Viewers

• UCSF ChimeraX — Next-generation molecular visualization program, following UCSF Chimera.

• wxMacMolPlt — An open-source GUI for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package.

Drawing

• Chemtool — GTK-based program for drawing chemical structural formulas.

• Marvin — Java-based program for drawing chemical structural formulas.

Modeling

• AmberTools — AmberTools consists of several independently developed packages that work well by themselves, and with Amber18 itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

• Fpocket — Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.

• GROMACS (GROningen MAchine for Chemical Simulations) — Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

• NAMD — NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

• PMEMD — PMEMD module of AMBER software package.

• RDKit — A collection of cheminformatics and machine-learning software written in C++ and Python.

Simulation analysis

• mdanalysis — An object-oriented python toolkit to analyze molecular dynamics trajectories in many popular formats.

• MDTraj — A modern, open library for the analysis of molecular dynamics trajectories.