# List of applications/Science

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## Contents

## Science

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

### Scientific documents

### Mathematics

#### Calculator

**bc**— Arbitrary precision calculator language.

**calc**— Arbitrary precision console calculator.

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

**galculator**— GTK+ based scientific calculator.

**GCalctool**— Scientific calculator included in the GNOME desktop.

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

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

**KCalc**— Scientific calculator included in the KDE desktop.

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

**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.

#### 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.

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

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

**Xcas**— User interface to Giac, a free, basic computer algebra system.

#### 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.

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

**Sage**— Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.

**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.

**RKWard**— Frontend for the statistical language R.

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

#### Data evaluation

**Extrema**— Visualization and data analysis tool.

**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.

**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.

**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).

**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.

**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.

**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).

#### Periodic table

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

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

#### 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).

#### 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.

**GIMP Astronomy Plugins**— Set of GIMP plugins for astronomical image processing.

**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.

**Open PHD Guiding**— Telescope autoguiding software based on the famous PHD Guiding.

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

**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.

**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.

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

### 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.

**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).

**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.

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

**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.

#### 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.

**SWMM**— Storm Water Management Model is a dynamic rainfall-runoff-subsurface runoff simulation model used for simulation of the surface/subsurface hydrology quantity and quality.

- http://www.epa.gov/ || swmm5-git
^{AUR}

#### 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.

**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.