List of applications/Science
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Science
Scientific documents
See the main article: List of applications/Documents#Scientific documents.
Mathematics
Calculator
See also Wikipedia:Comparison of software calculators.
- bc — Arbitrary precision calculator language.
- calc — Arbitrary precision console calculator.
- Extcalc — Qt-based scientfic graphical calculator.
- galculator — GTK+ based scientific calculator.
- GNOME Calculator — Scientific calculator included in the GNOME desktop.
- GCalctool — Scientific calculator included in the GNOME desktop (old GTK2 version).
- http://www.gnome.org || gcalctool-oldgui^{AUR}
- KAlgebra — Calculator and 3D plotter included in KDE EDU.
- KCalc — Scientific calculator included in the KDE desktop.
- Qalculate — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.
- SpeedCrunch — Fast, high precision and powerful cross-platform calculator.
- xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.
Computer algebra system
See also Wikipedia:Comparison of computer algebra systems.
- AXIOM — FriCAS: derivative of the powerful AXIOM-CAS
- http://fricas.sourceforge.net || fricas^{AUR}
- Fermat — Computer algebra system that does arithmetic of arbitrarily long integers and fractions, multivariate polynomials, symbolic calculations, matrices over polynomial rings, graphics, and other numerical calculations.
- http://home.bway.net/lewis/ || fermat^{AUR}^{[broken link: archived in aur-mirror]}
- GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.
- Maple — Famous commercial CAS. Often used in education.
- http://www.maplesoft.com/products/maple/ || not packaged? search in AUR
- 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.
- http://www.mathics.org/ || mathics^{AUR}
- Mathomatic — General purpose Computer Algebra System written in C.
- Maxima — Maple/Mathematica-like program with a wxWidgets based frontend.
- PARI/GP — Computer algebra system designed for fast computations in number theory.
- Xcas — User interface to Giac, a free, basic computer algebra system.
Scientific or technical computing
See also Wikipedia:Comparison of numerical analysis software.
- EngLab — Cross-compile mathematical platform with a C like syntax.
- http://englab.bugfest.net || englab^{AUR}
- Euler — Numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.
- http://euler.sourceforge.net || euler^{AUR}^{[broken link: archived in aur-mirror]}
- FreeMat — Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.
- GNU Radio — Software development toolkit that provides signal processing blocks to implement software radios.
- matplotlib (PyLab) — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
- Sage-mathematics — Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.
- Scilab — Matlab alternative used for numerical computations. Its syntax is not equivalent to that of Matlab, but it can be easily converted.
- http://www.scilab.org/ || scilab^{AUR}
Statistics
See also Wikipedia:Comparison of statistical packages.
- JAGS (Just another Gibbs sampler) — Cross-platform program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
- http://mcmc-jags.sourceforge.net/ || jags^{AUR}
- Python Data Analysis Library (pandas) — Providing high-performance, easy-to-use data structures and data analysis tools with Python programming language.
- PSPP — Free SPSS implementation.
- http://www.gnu.org/software/pspp/ || pspp^{AUR}
- R — Software environment for statistical computing and graphics.
- RKWard — Frontend for the statistical language R.
- http://rkward.sourceforge.net/ || rkward^{AUR}
- RStudio — A powerful and productive IDE for R written in Qt.
Data evaluation
See also Wikipedia:List of information graphics software.
- Extrema — Visualization and data analysis tool.
- http://sourceforge.net/projects/extrema || extrema^{AUR}^{[broken link: archived in aur-mirror]}
- Fityk — Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.
- http://fityk.nieto.pl/ || fityk^{AUR}
- Gnuplot — Command-line program that can generate 2D and 3D plots of functions, data, and data fits.
- Grace — WYSIWYG 2D graph plotting tool.
- http://plasma-gate.weizmann.ac.il/Grace/ || grace qtgrace^{AUR} gracegtk^{AUR}
- LabPlot — Free software data analysis and visualization application, similar to SciDAVis.
- http://labplot.sourceforge.net/ || labplot2^{AUR}^{[broken link: archived in aur-mirror]}
- QtiPlot — Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.
- ROOT — Data analysis program and library (originally for particle physics) developed by CERN.
- http://root.cern.ch/drupal/ || root^{AUR}
- SciDAVis — Fork of QtiPlot with the goal of being better documented and more user friendly.
- http://scidavis.sourceforge.net/ || scidavis^{AUR}
See also List of applications#Spreadsheets
Chemistry and biology
Computational biology and bioinformatics
See also Wikipedia:List of open source bioinformatics software.
- BALL (Biochemical Algorithms Library) — Application framework in C++ that provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.
- http://www.ball-project.org/ || ball^{AUR}
- BioJava — Set of Java tools for computational biology, as well as bioinformatics.
- http://biojava.org || biojava^{AUR}
- Biopython — Python package with tools for computational biology, as well as bioinformatics.
- EMBOSS (European Molecular Biology Open Software Suite) — Open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community.
- http://emboss.sourceforge.net/ || emboss^{AUR}
- MEGA (Molecular Evolutionary Genetics Analysis) — Integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.
- http://www.megasoftware.net/ || not packaged? search in AUR
- MUMmer — Bioinformatics software system for sequence alignment based on suffix trees.
- http://mummer.sourceforge.net/ || mummer^{AUR}
- UGENE — Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.
- http://ugene.unipro.ru/ || ugene^{AUR}
Molecules
Viewers
See also Wikipedia:List of molecular graphics systems.
- Avogadro — Editor, viewer and simulator for 3D molecule structures (also supports downloading files from the Protein Data Bank).
- BALLView — Standalone molecular modeling and visualization application, part of the BALL framework.
- http://www.ballview.org/ || ball^{AUR}
- Ghemical — Computational chemistry software package used to edit, view and simulate molecular structures.
- PyMOL — Open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.
- RasMol — Computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.
- http://www.rasmol.org/ || rasmol^{AUR}^{[broken link: archived in aur-mirror]}
Drawing
- BKChem — Practical and goodlooking skeletal formula molecule drawing program.
- http://bkchem.zirael.org/ || bkchem^{AUR}
- Chemtool — GTK+-based program for drawing chemical structural formulas.
- EasyChem — Simple skeletal formula molecule drawing program with a focus on producing press-quality figures.
- http://easychem.sourceforge.net/ || not packaged? search in AUR
- Gabedit — Graphical user interface to computational chemistry packages like GAMESS, Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, Firefly (previously PC GAMESS) and Q-Chem.
- http://gabedit.sourceforge.net/ || gabedit^{AUR}
- XDrawChem — Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).
- http://xdrawchem.sourceforge.net/ || xdrawchem^{AUR}^{[broken link: archived in aur-mirror]}
Modeling
- 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.
- http://www.gromacs.org || gromacs^{AUR}
- Quantum ESPRESSO — Integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
- http://www.quantum-espresso.org/ || quantum-espresso^{AUR}^{[broken link: archived in aur-mirror]}
Periodic table
- eperiodique — A simple Periodic Table Of Elements viewer using the EFL.
- gElemental — Periodic table of the elements with additional information.
- Kalzium — Periodic table of the elements with molecule editor and equation solver from the KDE desktop.
Biochemistry
- Bioclipse — Java-based visual platform for biochemistry that uses the Eclipse Rich Client Platform (RCP).
- http://www.bioclipse.net/ || not packaged? search in AUR
Image manipulation
- ImageJ — Java-based image processing and analysing program that provides extensibility via plugins and macros. It is widely used in microscopy (e.g. for cell counting).
- http://rsb.info.nih.gov/ij || imagej^{AUR}
- Fiji — ImageJ distribution (and soon ImageJ2) with a lot of plugins organized into a coherent menu structure.
- http://fiji.sc || fiji-binary^{AUR}
Astronomy
- Celestia — 3D astronomy simulation program that allows users to travel through an extensive universe, modeled after reality, at any speed, in any direction and at any time in history.
- GIMP Astronomy Plugins — Set of GIMP plugins for astronomical image processing.
- GoQat — Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.
- http://canburytech.net/GoQat/ || goqat^{AUR}
- KStars — Planetarium application that provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. It is included in KDE Edu.
- Open PHD Guiding — Telescope autoguiding software based on the famous PHD Guiding.
- http://code.google.com/p/open-phd-guiding/ || open-phd-guiding-svn^{AUR}^{[broken link: archived in aur-mirror]}
- Qastrocam-g2 — Webcam acquisition software for planetary imaging.
- Skychart / Cartes du Ciel — Planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.
- StarPlot — 3-dimensional star chart viewer.
- http://starplot.org/ || starplot^{AUR}
- Stellarium — Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.
- Where Is M13 — Application to visualize the locations and physical properties of deep sky objects.
- XEphem — Motif-based ephemeris and planetarium program.
Physics
Electronics
See also Wikipedia:Comparison of EDA software.
Digital logic
Digital logic software are mainly simple educational tools that intended for only designing and simulating logic circuits.
- atanua — Real time logic simulator.
- http://sol.gfxile.net/atanua/ || atanua^{AUR}^{[broken link: archived in aur-mirror]}
- eqntott — Utility to convert a set of boolean logic equations to a PLA-esque truth table.
- https://code.google.com/p/eqntott/ || eqntott^{AUR}^{[broken link: archived in aur-mirror]}
- espresso — Heuristic logic minimizer, reduces the amount of gates required for digital circuits.
- https://code.google.com/p/eqntott/ || espresso^{AUR}^{[broken link: archived in aur-mirror]}
- giraffe — A simple logic circuit simulator written in Java.
- http://nbenoit.tuxfamily.org/ || giraffe^{AUR}^{[broken link: archived in aur-mirror]}
- glogic — An educational graphical logic circuit simulator.
- https://launchpad.net/glogic || glogic^{AUR}
- KLogic — Digital logic design and simulation software for KDE which also simulate karnaugh diagrams.
- http://www.a-rostin.de/ || klogic^{AUR}^{[broken link: archived in aur-mirror]}
- Logisim — Educational digital logic design and simulation software, written in Java, officially its development has stopped.
- Logisim Evolution — Project which continue the development of the original Logisim with new features, written in Java.
- https://github.com/reds-heig/logisim-evolution || logisim-evolution^{AUR}^{[broken link: archived in aur-mirror]}
- SmartSim — Simple and beautiful digital logic circuit design and simulation software, mainly target teachers and students, very lightweight and cross platform, GPL licensed, written in Vala.
- http://smartsim.org.uk || smartsim-git^{AUR}
HDL
- Altera Design Software — A set of design tools for Altera's FPGA chips that includes Quartus II and ModelSim-Altera.
- Xilinx ISE WebPACK — FPGA programmable logic design suit.
- http://www.xilinx.com/products/design-tools/ise-design-suite/ise-webpack.html || see Xilinx ISE WebPACK
MCU IDE
- Arduino — Arduino prototyping platform SDK.
- KTechLab — IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.
- http://sourceforge.net/projects/ktechlab/ || ktechlab-zoltan_p-git^{AUR}^{[broken link: archived in aur-mirror]}
Schematic capture editor
- gEDA — Full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.
- KiCAD — Software suite for electronic design automation (EDA) that facilitates the design of schematics for electronic circuits and their conversion to PCB (printed circuit board).
- Oregano — Graphical software application for schematic capture and simulation of electrical circuits. The actual simulation is done by the ngspice or Gnucap engines.
- https://github.com/drahnr/oregano || oregano^{AUR}
- QElectroTech — Application used to draw advanced electrical circuits.
- http://qelectrotech.org/ || qelectrotech^{AUR}
- Qucs — Electronics circuit simulator application that gives you the ability to set up a circuit with a graphical user interface and simulate its large-signal, small-signal and noise behaviour.
Physics simulation
- Code_Aster — Software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.
- EPANET — EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.
- http://www.epa.gov/ || epanet2-git^{AUR}
- Step — Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.
- SWMM — Storm Water Management Model is a dynamic rainfall-runoff-subsurface runoff simulation model used for simulation of the surface/subsurface hydrology quantity and quality.
- http://www.epa.gov/ || swmm5-git^{AUR}
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.
- http://convertall.bellz.org/ || convertall^{AUR}
- Gonvert — Conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.
- Units — Command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.
Geography
- GNOME Maps — A simple map client for GNOME. Part of gnome-extra.
- JOSM — An editor for OpenStreetMap written in Java.
- Marble — Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of kdeedu.
- Merkaartor — OpenStreetMap editor.
- Viking — GTK+2 application to manage GPS data.