List of applications/Science

Science

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

Mathematics

Calculator

• 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/ || extcalc^AUR

• GCalctool — Scientific calculator included in the GNOME desktop.

http://www.gnome.org || gcalctool-oldgui^AUR

• 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 || speedcrunch^AUR

• xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.

http://xorg.freedesktop.org/ || xorg-xcalc

Computer algebra system

• 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

• GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.

http://www.gap-system.org || gap-math^AUR

• Mathomatic — General purpose Computer Algebra System written in C.

http://www.mathomatic.org/ || mathomatic

• Maxima — Maple/Mathematica-like program with a wxWidgets based frontend.

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 || xcas^AUR

Scientific or technical computing

• 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

• 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

• Octave — Matlab-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/ || scilab^AUR

Statistics

• 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

• PSPP — Free SPSS implementation.

http://www.gnu.org/software/pspp/ || pspp^AUR

• 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/ || rkward^AUR

Data evaluation

• Extrema — Visualization and data analysis tool.

http://sourceforge.net/projects/extrema || extrema^AUR

• 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.

http://www.gnuplot.info/ || gnuplot

• 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

• 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/ || 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

• 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/ || ball^AUR

• BioJava — Set of Java tools for computational biology, as well as bioinformatics.

http://biojava.org/wiki/Main_Page || biojava^AUR

• Biopython — Python package with tools for computational biology, as well as bioinformatics.

http://biopython.org/wiki/Biopython || python-biopython^AUR python2-biopython^AUR

• 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/ || mega^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

Molecule viewer

• 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/ || ball^AUR

• Ghemical — Computational chemistry software package used to edit, view and simulate molecular structures.

http://bioinformatics.org/ghemical/ghemical/index.html || ghemical^AUR

• 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 || pymol^AUR

• 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

Molecule 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.

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

• 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

Periodic table

• gElemental — Periodic table of the elements with additional information.

http://freshmeat.net/projects/gelemental || gelemental^AUR

• 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 || 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

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.

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-astronomy^AUR

• 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.

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-svn^AUR

• Qastrocam-g2 — Webcam acquisition software for planetary imaging.

http://sourceforge.net/projects/qastrocam-g2/ || qastrocam-g2^AUR

• 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/ || skychart^AUR

• 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.

http://www.stellarium.org/ || stellarium

• XEphem — Motif-based ephemeris and planetarium program.

http://www.clearskyinstitute.com/xephem/xephem.html || xephem^AUR

Physics

Electronics

• 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/ || klogic^AUR

• 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 || 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.

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 || aster^AUR

• 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/ || convertall^AUR

• 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/ || gonvert^AUR

• 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