# Difference between revisions of "List of applications/Science"

(→Physics Simulation: phrasing. wikipedia links.) |
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==== Unit Conversion ==== | ==== Unit Conversion ==== | ||

− | * {{App| | + | * {{App|ConvertAll|A 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/|{{AUR|convertall}}}} |

− | * {{App|Gonvert| | + | * {{App|Gonvert|A 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/|{{AUR|gonvert}}}} |

− | * {{App|Units| | + | * {{App|[[Wikipedia:GNU Units|Units]]|A 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/|{{Pkg|units}}}} |

## Revision as of 09:02, 9 September 2012

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

## Contents

## Science

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

### Scientific Documents

### Mathematics

#### Calculator

**bc**— An arbitrary precision calculator language.

**calc**— An arbitrary precision console calculator.

**Extcalc**— A Qt based scientfic graphical calculator.

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

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

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

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

**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.

#### 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.

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

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

**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.

#### 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.

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

**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.

**RKWard**— A frontend for the statistical language R.

- http://rkward.sourceforge.net/ || rkward
^{AUR}

#### Data Evaluation

**Extrema**— A visualization and data analysis tool.

**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.

**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.

**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.

**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**— An editor, viewer and simulator for 3D molecule structures (also supports downloading files from the Protein Data Bank).

**BALLView**— A standalone molecular modeling and visualization application, part of the BALL framework.

- http://www.ballview.org/ || ball
^{AUR}

**Ghemical**— A computational chemistry software package used to edit, view and simulate molecular structures.

**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/ || pymol
^{AUR}

**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/ || rasmol
^{AUR}

#### Molecule Drawing

**BKChem**— A practical and goodlooking skeletal formula molecule drawing program.

- http://bkchem.zirael.org/ || bkchem
^{AUR}

**Chemtool**— A GTK+ based program for drawing chemical structural formulas.

**EasyChem**— A simple skeletal formula molecule drawing program with a focus on producing press-quality figures.

- http://easychem.sourceforge.net/ || easychem
^{AUR}

**Gabedit**— A 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**— An extensive skeletal formula molecule drawing program (includes spectroscopy prediction).

#### Periodic Table

**gElemental**— A periodic table of the elements with additional information.

**Kalzium**— A periodic table of the elements with molecule editor and equation solver from the KDE desktop.

#### Biochemistry

**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 || gromacs
^{AUR}

**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).

#### Image manipulation

**ImageJ**— A 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}

### Astronomy

**Celestia**— A 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**— A set of GIMP plugins for astronomical image processing.

**KStars**— A 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.

**Skychart / Cartes Du Ciel**— A 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**— A 3-dimensional star chart viewer.

- http://starplot.org/ || starplot
^{AUR}

**Stellarium**— A beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.

**XEphem**— A Motif based ephemeris and planetarium program.

### Physics

#### Electronics

**gEDA**— A full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.

**KiCAD**— A software suite for electronic design automation (EDA) that facilitates the design of schematics for electronic circuits and their conversion to PCB (printed circuit board).

**KLogic**— An application used for easily building and simulating digital circuits.

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

**KTechLab**— An 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.

**Oregano**— A graphical software application for schematic capture and simulation of electrical circuits. The actual simulation is done by the ngspice or Gnucap engines.

**QElectroTech**— An application used to draw advanced electrical circuits.

- http://qelectrotech.org/ || qelectrotech
^{AUR}

**Qucs**— An 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**— A software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.

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

**Step**— A two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.

#### Unit Conversion

**ConvertAll**— A 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**— A conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.

**Units**— A command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.