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 — An arbitrary precision calculator language.

http://www.gnu.org/software/bc/ || bc

• calc — An arbitrary precision console calculator.

http://www.isthe.com/chongo/tech/comp/calc/ || calc

• Extcalc — A Qt based scientfic graphical calculator.

http://extcalc-linux.sourceforge.net/ || extcalc^AUR

• GCalctool — A scientific calculator included in the GNOME desktop.

http://www.gnome.org || gcalctool

• KAlgebra — A calculator and 3D plotter included in KDE EDU.

http://www.kde.org/applications/education/kalgebra/ || kdeedu-kalgebra

• KCalc — A scientific calculator included in the KDE desktop.

http://kde.org/applications/utilities/kcalc/ || kdeutils-kcalc

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

http://qalculate.sourceforge.net/ || libqalculate

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

http://speedcrunch.org || speedcrunch^AUR

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

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

Computer Algebra System

• Fermat — A 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

• Mathomatic — A general purpose Computer Algebra System written in C.

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

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

http://maxima.sourceforge.net/ || maxima wxmaxima

• PARI/GP — A computer algebra system designed for fast computations in number theory.

http://pari.math.u-bordeaux.fr/ || pari

• Sage — A algebra system similar to Maxima, but written in Python.

http://www.sagemath.org/ || sage-mathematics^AUR

• Xcas — A 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 — A cross-compile mathematical platform with a C like syntax.

http://englab.bugfest.net || englab^AUR

• Euler — A 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 — A 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 — A Matlab-like language and interface for numerical computations.

http://www.gnu.org/software/octave/ || octave

• PyLab — A collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.

http://www.scipy.org/PyLab || python2-matplotlib

• Scilab — A 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) — A cross-platform program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

http://mcmc-jags.sourceforge.net/ || jags^AUR

• PSPP — A free SPSS implementation.

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

• R — A software environment for statistical computing and graphics.

http://cran.r-project.org/ || r

• RKWard — A frontend for the statistical language R.

http://rkward.sourceforge.net/ || rkward^AUR

Data Evaluation

• Extrema — A visualization and data analysis tool.

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

• Fityk — A curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.

http://www.unipress.waw.pl/fityk/ || fityk^AUR

• Gnuplot — A command-line program that can generate 2D and 3D plots of functions, data, and data fits.

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

• Grace — A WYSIWYG 2D graph plotting tool.

http://plasma-gate.weizmann.ac.il/Grace/ || grace qtgrace^AUR gracegtk^AUR

• LabPlot — A free software data analysis and visualization application, similar to SciDAVis.

http://labplot.sourceforge.net/ || labplot2^AUR

• QtiPlot — A 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 — A data analysis program and library (originally for particle physics) developed by CERN.

http://root.cern.ch/drupal/ || root^AUR

• SciDAVis — A fork of QtiPlot with the goal of being better documented and more user friendly.

http://scidavis.sourceforge.net/ || scidavis^AUR

See also Common Applications#Spreadsheets

Chemistry and Biology

Computational Biology and Bioinformatics

• BALL (Biochemical Algorithms Library) — An 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 — A set of Java tools for computational biology, as well as bioinformatics.

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

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

http://biopython.org/wiki/Biopython || biopython^AUR

• EMBOSS (European Molecular Biology Open Software Suite) — An 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) — An 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 — A bioinformatics software system for sequence alignment based on suffix trees.

http://mummer.sourceforge.net/ || mummer^AUR

• UGENE — An 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 — edit and view 3D molecule structures (also .pdb) and simulate

http://avogadro.openmolecules.net/wiki/Main_Page || avogadro

• Ballview — standalone molecular modeling and visualization application

http://www.ballview.org/ || ball^AUR

• Ghemical — edit and view 3D molecule structures (also .pdb) and simulate

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

• Rasmol — view 3D molecule structures

http://www.rasmol.org/ || rasmol^AUR

• Pymol — view 3D molecule structures

http://pymol.sourceforge.net/ || pymol^AUR

Molecule Drawing

• BKchem — practical and goodlooking skeletal formula molecule drawing program

http://bkchem.zirael.org/ || bkchem^AUR

• XDrawChem — extensive skeletal formula molecule drawing program (incl. spectroscopy prediction)

http://xdrawchem.sourceforge.net/ || xdrawchem^AUR

• EasyChem — simple skeletal formula molecule drawing program

http://easychem.sourceforge.net/ || easychem^AUR

• Chemtool — skeletal formula molecule drawing program

http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html || chemtool

• Gabedit — graphical user interface to computational chemistry packages like Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, Orca, PCGamess and hem

http://gabedit.sourceforge.net/ || gabedit^AUR

Periodic Table

• Kalzium — periodic table of the elements with molecule editor and equation solver from the KDE project

http://edu.kde.org/kalzium/ || kdeedu-kalzium

• gElemental — periodic table of the elements and additional information

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

Biochemistry

• Bioclipse — Aims to be a complete biochemistry office suite.

http://www.bioclipse.net/ || not packaged? search in AUR

Molecular Modeling

• GROMACS — 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 computer codes for electronic-structure calculations and materials modeling at the 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. Widely used in microscopy (e.g. for cell counting).

http://rsb.info.nih.gov/ij || imagej^AUR

Astronomy

• Cartes Du Ciel — aka 'Skychart' - Planetarium,Sky mapping & Telescope control

http://www.ap-i.net/skychart/start/ || skychart^AUR

• Celestia — space simulation software

http://www.shatters.net/celestia/ || celestia

• GIMP Plugins Astronomy- GIMP plugins for astronomical images, overlay mode, darkness subtraction, merge images and others gimp-plugin-astronomy^AUR
• Exphem — Ephemeris & Planetarium program

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

• KStars — KDE desktop planetarium

http://edu.kde.org/kstars/ || kdeedu-kstars

• StarPlot — 3D starchart viewer

http://starplot.org/ || starplot^AUR

• Stellarium — beautiful 3D planetarium

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

Physics

Electronics

• gEDA — electronic design automation tools

http://www.gpleda.org || geda-gaf

• Qucs — electronic circuit simulation

http://qucs.sourceforge.net/ || qucs

• Oregano — electronic circuit simulation

https://gitorious.org/oregano || oregano^AUR

• QElectroTech — draw advanced electrical circuits

http://qelectrotech.org/ || qelectrotech^AUR

• KiCAD — design schematics for printed circuit boards

http://kicad.sourceforge.net/wiki/index.php/Main_Page || kicad^AUR

• KSimus — logical circuits simulation

http://ksimus.berlios.de/ || ksimus^AUR

• KLogic — logical circuits simulation

http://www.a-rostin.de/ || klogic^AUR

Physics Simulation

• Aster — simulation for civil and structural engineering

http://www.code-aster.org || aster^AUR

• Step — physics Simulation Educative physics simulation (KDE)

http://edu.kde.org/step/ || kdeedu-step

Unit Conversion

• Convertall — convert between different physical units

http://convertall.bellz.org/ || convertall^AUR

• Gonvert — convert between different physical units

http://www.unihedron.com/projects/gonvert/ || gonvert^AUR

• Units — CLI Unit converter and calculator

http://www.gnu.org/s/units/ || units