Difference between revisions of "List of applications/Science"

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==== Molecular Modeling ====
==== Molecular Modeling ====
* {{App|[[Wikipedia:GROMACS|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|{{AUR|gromacs}}}}  
* {{App|[[Wikipedia:GROMACS|GROMACS]] (GROningen MAchine for Chemical Simulations)|A 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|{{AUR|gromacs}}}}  
* {{App|[[Wikipedia:Quantum ESPRESSO|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/|{{AUR|quantum-espresso}}}}
* {{App|[[Wikipedia:Quantum ESPRESSO|Quantum ESPRESSO]]|An 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/|{{AUR|quantum-espresso}}}}
==== Image manipulation ====
==== Image manipulation ====

Revision as of 08:09, 9 September 2012

zh-CN:Common Applications/Science Template:Common Applications navigation


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

Scientific Documents





  • 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/ || extcalcAUR
  • 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 || speedcrunchAUR
  • 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/ || fermatAUR
  • Mathomatic — A general purpose Computer Algebra System written in C.
http://www.mathomatic.org/math/ || mathomatic
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-mathematicsAUR
  • Xcas — A user interface to Giac, a free, basic computer algebra system.
http://www-fourier.ujf-grenoble.fr/~parisse/giac.html || xcasAUR

Scientific or Technical Computing


  • EngLab — A cross-compile mathematical platform with a C like syntax.
http://englab.bugfest.net || englabAUR
  • 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 || eulerAUR
  • 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/ || scilabAUR



  • 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/ || jagsAUR
  • PSPP — A free SPSS implementation.
http://www.gnu.org/software/pspp/ || psppAUR
  • 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/ || rkwardAUR

Data Evaluation


  • Extrema — A visualization and data analysis tool.
http://sourceforge.net/projects/extrema || extremaAUR
  • 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/ || fitykAUR
  • 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 qtgraceAUR gracegtkAUR
  • LabPlot — A free software data analysis and visualization application, similar to SciDAVis.
http://labplot.sourceforge.net/ || labplot2AUR
  • 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/ || rootAUR
  • SciDAVis — A fork of QtiPlot with the goal of being better documented and more user friendly.
http://scidavis.sourceforge.net/ || scidavisAUR

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/ || ballAUR
  • BioJava — A set of Java tools for computational biology, as well as bioinformatics.
http://biojava.org/wiki/Main_Page || biojavaAUR
  • Biopython — A Python package with tools for computational biology, as well as bioinformatics.
http://biopython.org/wiki/Biopython || biopythonAUR
  • 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/ || embossAUR
  • 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/ || megaAUR
  • MUMmer — A bioinformatics software system for sequence alignment based on suffix trees.
http://mummer.sourceforge.net/ || mummerAUR
  • 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/ || ugeneAUR

Molecule Viewer


  • Avogadro — An 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 — A standalone molecular modeling and visualization application, part of the BALL framework.
http://www.ballview.org/ || ballAUR
  • Ghemical — A computational chemistry software package used to edit, view and simulate molecular structures.
http://bioinformatics.org/ghemical/ghemical/index.html || ghemical
  • PyMOL — An open-source molecular visualization system that can produce high quality 3D images of small molecules and biological macromolecules, such as proteins.
http://pymol.sourceforge.net/ || pymolAUR
  • RasMol — A 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 — A practical and goodlooking skeletal formula molecule drawing program.
http://bkchem.zirael.org/ || bkchemAUR
  • Chemtool — A GTK+ based program for drawing chemical structural formulas.
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html || chemtool
  • EasyChem — A simple skeletal formula molecule drawing program with a focus on producing press-quality figures.
http://easychem.sourceforge.net/ || easychemAUR
http://gabedit.sourceforge.net/ || gabeditAUR
  • XDrawChem — An extensive skeletal formula molecule drawing program (includes spectroscopy prediction).
http://xdrawchem.sourceforge.net/ || xdrawchemAUR

Periodic Table

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


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

Molecular Modeling

  • GROMACS (GROningen MAchine for Chemical Simulations) — A 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 — An 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. Widely used in microscopy (e.g. for cell counting).
http://rsb.info.nih.gov/ij || imagejAUR


  • Cartes Du Ciel — aka 'Skychart' - Planetarium,Sky mapping & Telescope control
http://www.ap-i.net/skychart/start/ || skychartAUR
http://www.shatters.net/celestia/ || celestia
http://www.clearskyinstitute.com/xephem/xephem.html || xephemAUR
  • KStars — KDE desktop planetarium
http://edu.kde.org/kstars/ || kdeedu-kstars
  • StarPlot — 3D starchart viewer
http://starplot.org/ || starplotAUR
http://www.stellarium.org/ || stellarium



  • 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 || oreganoAUR
  • QElectroTech — draw advanced electrical circuits
http://qelectrotech.org/ || qelectrotechAUR
  • KiCAD — design schematics for printed circuit boards
http://kicad.sourceforge.net/wiki/index.php/Main_Page || kicadAUR
  • KSimus — logical circuits simulation
http://ksimus.berlios.de/ || ksimusAUR
  • KLogic — logical circuits simulation
http://www.a-rostin.de/ || klogicAUR

Physics Simulation

  • Aster — simulation for civil and structural engineering
http://www.code-aster.org || asterAUR
  • 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/ || convertallAUR
  • Gonvert — convert between different physical units
http://www.unihedron.com/projects/gonvert/ || gonvertAUR
  • Units — CLI Unit converter and calculator
http://www.gnu.org/s/units/ || units