List of applications/Science

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Science

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

Scientific documents

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Mathematics

Calculator

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  • bc — Arbitrary precision calculator language.
http://www.gnu.org/software/bc/ || bc
  • calc — Arbitrary precision console calculator.
http://www.isthe.com/chongo/tech/comp/calc/ || calc
  • Extcalc — Qt-based scientfic graphical calculator.
http://extcalc-linux.sourceforge.net/ || extcalcAUR
  • GCalctool — Scientific calculator included in the GNOME desktop.
http://www.gnome.org || gcalctool-oldguiAUR
  • KAlgebra — Calculator and 3D plotter included in KDE EDU.
http://www.kde.org/applications/education/kalgebra/ || kdeedu-kalgebra
  • KCalc — Scientific calculator included in the KDE desktop.
http://kde.org/applications/utilities/kcalc/ || kdeutils-kcalc
  • Qalculate — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.
http://qalculate.sourceforge.net/ || libqalculate
  • SpeedCrunch — Fast, high precision and powerful cross-platform calculator.
http://speedcrunch.org || speedcrunchAUR
  • xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.
http://xorg.freedesktop.org/ || xorg-xcalc

Computer algebra system

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  • 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/ || fermatAUR
  • GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.
http://www.gap-system.org || gap-mathAUR
  • Mathomatic — General purpose Computer Algebra System written in C.
http://www.mathomatic.org/ || mathomatic
http://maxima.sourceforge.net/ || maxima wxmaxima
  • PARI/GP — Computer algebra system designed for fast computations in number theory.
http://pari.math.u-bordeaux.fr/ || pari
  • Xcas — User interface to Giac, a free, basic computer algebra system.
http://www-fourier.ujf-grenoble.fr/~parisse/giac.html || xcasAUR

Scientific or technical computing

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  • EngLab — Cross-compile mathematical platform with a C like syntax.
http://englab.bugfest.net || englabAUR
  • Euler — Numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.
http://euler.sourceforge.net || eulerAUR
  • 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.
http://freemat.sourceforge.net/ || freemat
  • OctaveMatlab-like language and interface for numerical computations.
http://www.gnu.org/software/octave/ || octave
  • PyLab — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
http://www.scipy.org/PyLab || python2-matplotlib
  • Sage — Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.
http://www.sagemath.org || sage-mathematics
  • 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/ || scilabAUR

Statistics

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  • 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/ || jagsAUR
  • PSPP — Free SPSS implementation.
http://www.gnu.org/software/pspp/ || psppAUR
  • R — Software environment for statistical computing and graphics.
http://cran.r-project.org/ || r
  • RKWard — Frontend for the statistical language R.
http://rkward.sourceforge.net/ || rkwardAUR

Data evaluation

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  • Extrema — Visualization and data analysis tool.
http://sourceforge.net/projects/extrema || extremaAUR
  • Fityk — Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.
http://fityk.nieto.pl/ || fitykAUR
  • Gnuplot — Command-line program that can generate 2D and 3D plots of functions, data, and data fits.
http://www.gnuplot.info/ || gnuplot
  • Grace — WYSIWYG 2D graph plotting tool.
http://plasma-gate.weizmann.ac.il/Grace/ || grace qtgraceAUR gracegtkAUR
  • LabPlot — Free software data analysis and visualization application, similar to SciDAVis.
http://labplot.sourceforge.net/ || labplot2AUR
  • QtiPlot — Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.
http://soft.proindependent.com/qtiplot.html || qtiplot
  • ROOT — Data analysis program and library (originally for particle physics) developed by CERN.
http://root.cern.ch/drupal/ || rootAUR
  • SciDAVis — Fork of QtiPlot with the goal of being better documented and more user friendly.
http://scidavis.sourceforge.net/ || scidavisAUR

See also List of Applications#Spreadsheets

Chemistry and biology

Computational biology and bioinformatics

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  • BALL (Biochemical Algorithms Library) — Application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.
http://www.ball-project.org/ || ballAUR
  • BioJava — Set of Java tools for computational biology, as well as bioinformatics.
http://biojava.org/wiki/Main_Page || biojavaAUR
  • Biopython — Python package with tools for computational biology, as well as bioinformatics.
http://biopython.org/wiki/Biopython || python-biopythonAUR python2-biopythonAUR
  • 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/ || embossAUR
  • 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/ || megaAUR
  • MUMmer — Bioinformatics software system for sequence alignment based on suffix trees.
http://mummer.sourceforge.net/ || mummerAUR
  • UGENE — Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.
http://ugene.unipro.ru/ || ugeneAUR

Molecule viewer

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  • Avogadro — Editor, viewer and simulator for 3D molecule structures (also supports downloading files from the Protein Data Bank).
http://avogadro.openmolecules.net/wiki/Main_Page || avogadro
  • BALLView — Standalone molecular modeling and visualization application, part of the BALL framework.
http://www.ballview.org/ || ballAUR
  • Ghemical — Computational chemistry software package used to edit, view and simulate molecular structures.
http://bioinformatics.org/ghemical/ghemical/index.html || ghemicalAUR
  • PyMOL — Open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.
http://pymol.org || pymolAUR
  • 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/ || rasmolAUR

Molecule drawing

  • BKChem — Practical and goodlooking skeletal formula molecule drawing program.
http://bkchem.zirael.org/ || bkchemAUR
  • Chemtool — GTK+-based program for drawing chemical structural formulas.
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html || chemtool
  • EasyChem — Simple skeletal formula molecule drawing program with a focus on producing press-quality figures.
http://easychem.sourceforge.net/ || not packaged? search in AUR
http://gabedit.sourceforge.net/ || gabeditAUR
  • XDrawChem — Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).
http://xdrawchem.sourceforge.net/ || xdrawchemAUR

Periodic table

  • gElemental — Periodic table of the elements with additional information.
http://freshmeat.net/projects/gelemental || gelementalAUR
  • Kalzium — Periodic table of the elements with molecule editor and equation solver from the KDE desktop.
http://edu.kde.org/kalzium/ || kdeedu-kalzium

Biochemistry

  • Bioclipse — Java-based visual platform for biochemestry that uses the Eclipse Rich Client Platform (RCP).
http://www.bioclipse.net/ || not packaged? search in AUR

Molecular 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 || gromacsAUR
  • 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-espressoAUR

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 || imagejAUR
  • Fiji — ImageJ distribution (and soon ImageJ2) with a lot of plugins organized into a coherent menu structure.
http://fiji.sc || fiji-binaryAUR

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.
http://www.shatters.net/celestia/ || celestia
  • GIMP Astronomy Plugins — Set of GIMP plugins for astronomical image processing.
http://hennigbuam.de/georg/gimp.html || gimp-plugin-astronomyAUR
  • GoQat — Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.
http://canburytech.net/GoQat/ || goqatAUR
  • 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.
http://edu.kde.org/kstars/ || kdeedu-kstars
  • Open PHD Guiding — Telescope autoguiding software based on the famous PHD Guiding.
http://code.google.com/p/open-phd-guiding/ || open-phd-guiding-svnAUR
  • Qastrocam-g2 — Webcam acquisition software for planetary imaging.
http://sourceforge.net/projects/qastrocam-g2/ || qastrocam-g2AUR
  • 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.
http://www.ap-i.net/skychart/start/ || skychartAUR
  • StarPlot — 3-dimensional star chart viewer.
http://starplot.org/ || starplotAUR
  • Stellarium — Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.
http://www.stellarium.org/ || stellarium
  • XEphem — Motif-based ephemeris and planetarium program.
http://www.clearskyinstitute.com/xephem/xephem.html || xephemAUR

Physics

Electronics

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  • gEDA — Full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.
http://www.geda-project.org/ || geda-gaf
  • 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).
http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite || kicad
  • KLogic — Application used for easily building and simulating digital circuits.
http://www.a-rostin.de/ || klogicAUR
  • 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
  • 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/marc-lorber/oregano || oreganoAUR
  • QElectroTech — Application used to draw advanced electrical circuits.
http://qelectrotech.org/ || qelectrotechAUR
  • 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.
http://qucs.sourceforge.net/ || qucs

Physics simulation

  • Code_Aster — Software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.
http://www.code-aster.org || asterAUR
  • Step — Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.
http://edu.kde.org/step/ || kdeedu-step

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/ || convertallAUR
  • Gonvert — Conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.
http://www.unihedron.com/projects/gonvert/ || gonvertAUR
  • 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.
http://www.gnu.org/s/units/ || units