# List of applications/Science

## Contents

## Science

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

### Mathematics

#### Calculator

See also Wikipedia:Comparison of software calculators.

**bc**— Arbitrary precision calculator language.

**calc**— Arbitrary precision console calculator.

**Deepin Calculator**— Easy to use calculator for Deepin desktop.

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

**FOX Calculator**— Simple desktop calculator.

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

- http://galculator.mnim.org/ || GTK+ 3: galculator, GTK+ 2: galculator-gtk2

**Genius**— Advanced calculator including a mathematical programming language.

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

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

**Liri Calculator**— Calculator for Liri.

**MATE Calc**— Calculator for the MATE desktop environment.

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

**SpeedCrunch**— Fast, high precision and powerful cross-platform calculator.

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

#### Computer algebra system

See also Wikipedia:Comparison of computer algebra systems.

**AXIOM**— FriCAS: derivative of the powerful AXIOM-CAS

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

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

**Maple**— Famous commercial CAS. Often used in education.

**Mathics**— A free CAS for symbolic mathematical computations which uses Python as its main language. It aims at achieving a Mathematica-compatible syntax and functions. It relies mostly on Sympy for most mathematical tasks and, optionally, Sage for more advanced functionality.

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

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

**Maxima**— Maple/Mathematica-like computer algebra system.

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

**Singular**— Computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.

**wxMaxima**— Graphical user interface for Maxima being a powerful computer algebra system.

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

#### Scientific or technical computing

See also Wikipedia:Comparison of numerical analysis software.

**Cantor**— Application that lets you use your favorite mathematical applications from within a nice KDE-integrated Worksheet Interface. Part of kdeedu.

**EngLab**— Cross-compile mathematical platform with a C like syntax.

- http://englab.bugfest.net || englab
^{AUR}

**FFTW**— A Fast Fourier Transform library for computing discrete Fourier transforms. Used for a wide variety of numerical applications, which includes spectral methods.

- https://www.fftw.org/ || fftw fftw-mpi
^{AUR}fftw-mpich^{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
^{AUR}

**GeoGebra**— Dynamic mathematics software with interactive graphics, algebra and spreadsheet

**Julia**— High-level, high-performance dynamic language for technical computing.

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

**SageMath**— 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}, scilab-bin^{AUR}, scilab-git^{AUR}

#### Statistics

See also Wikipedia:Comparison of statistical packages.

**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}

**jamovi**— Statistics package, which is easy to use, and designed to be familiar to users of SPSS. Based on the Electron platform.

- https://www.jamovi.org/ || jamovi-git
^{AUR}

**Python Data Analysis Library (pandas)**— Providing high-performance, easy-to-use data structures and data analysis tools with Python programming language.

**PSPP**— Free SPSS implementation.

- https://www.gnu.org/software/pspp/ || pspp
^{AUR}

**R**— Software environment for statistical computing and graphics.

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

- https://rkward.kde.org/ || rkward
^{AUR}

**RStudio**— A powerful and productive IDE for R written in Qt.

#### Data analysis and plotting

See also Wikipedia:List of information graphics software.

**Engauge Digitizer**— Extracts data points from images of graphs.

**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
^{AUR}qtgrace^{AUR}gracegtk^{AUR}

**LabPlot**— Free software data analysis and visualization application, similar to SciDAVis.

**QtiPlot**— Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.

- http://www.qtiplot.com/ || qtiplot-git
^{AUR}^{[broken link: package not found]}

**Rocs**— Graph Theory IDE for everybody interested in designing and analyzing graph algorithms (e.g., lecturers, students, researchers). Part of kdeedu.

**ROOT**— Data analysis program and library (originally for particle physics) developed by CERN.

**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/Documents#Spreadsheets

#### Proof assistants

See also Wikipedia:Proof assistant.

**Agda**— Dependently typed functional programming language and proof assistant. It is an interactive system for writing and checking proofs.

**Coq**— Formal proof management system. It provides a formal language to write mathematical definitions, executable algorithms and theorems together with an environment for semi-interactive development of machine-checked proofs.

- https://coq.inria.fr/ || CLI: coq, GUI: coqide

**Isabelle**— Generic proof assistant that allows mathematical formulas to be expressed in a formal language and provides tools for proving those formulas in a logical calculus.

### Physics

#### Physics simulation

**Code_Aster**— Software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.

**EPANET**— EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.

- https://www.epa.gov/ || epanet2-git
^{AUR}

**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.

- https://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.

### Chemistry

#### Molecules

##### Viewers

See also Wikipedia:List of molecular graphics systems.

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

- http://avogadro.cc/ || avogadro
^{AUR}

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

- http://www.ball-project.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.

##### 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}

##### 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).

#### Periodic table

**eperiodique**— A simple Periodic Table Of Elements viewer using the EFL.

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

**Kalzium**— Periodic table of the elements with molecule editor and equation solver. Part of kdeedu.

### Earth science

#### Geography

**BT747**— The swiss army knife for MTK GPS dataloggers.

**FoxtrotGPS**— Lightweight and fast mapping application.

- https://www.foxtrotgps.org/ || foxtrotgps
^{AUR}

**Gebabbel**— Alternative GUI for GPSBabel.

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

**Geotag**— Match date/time information from photos with location information from a GPS unit or from a map.

**GNOME Maps**— A simple map client for GNOME. Part of gnome-extra.

**GottenGeography**— Easy to use photo geotagging application for the GNOME desktop.

**Gpredict**— Real-time satellite tracking and orbit prediction application.

- http://gpredict.oz9aec.net/ || gpredict
^{AUR}

**GPSBabel**— Reads, writes, and manipulates GPS waypoints, tracks, routes in a variety of formats.

**GPSCorrelate**— Correlate (geotagging) digital camera photos with GPS data in GPX format.

**gpsd**— Service daemon that monitors one or more GPSes or AIS receivers attached to a host computer through serial or USB ports, making all data on the location/course/velocity of the sensors available to be queried on TCP port 2947 of the host computer.

**GpsPrune**— View, edit and convert coordinate data from GPS systems.

**GPXSee**— GPS log file viewer and analyzer.

**GPX Viewer**— Simple tool to visualize tracks and waypoints stored in a gpx file.

**GRASS GIS**— Geospatial data management and analysis, image processing, graphics/maps production, spatial modeling and visualization.

- https://grass.osgeo.org/ || grass
^{AUR}

**gvSIG**— vSIG is a geographic information system (GIS), that is, a desktop application designed for capturing, storing, handling, analyzing and deploying any kind of referenced geographic information in order to solve complex management and planning problems.

- http://www.gvsig.com/en || gvsig-desktop-bin
^{AUR}

**JOSM**— Main editor for OpenStreetMap written in Java.

**Mapton**— Extensible desktop map and globe application written in Java.

- https://mapton.org/ || mapton
^{AUR}

**Marble**— Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of kdeedu.

- https://marble.kde.org/ || KDE: marble, Qt: marble-qt

**Merkaartor**— OpenStreetMap editor.

**Navit**— Modular turn-by-turn car navigation system.

**OffRoad**— Offline vector map display ported from OsmAnd.

**OpenOrienteering Mapper**— Orienteering mapmaking program.

**QMapShack**— Plan your next outdoor trip.

**QGIS**— Geographic Information System (GIS) that supports vector, raster & database formats.

**Subsurface**— Diving logbook to keep track of your dives by logging dive locations (with GPS coordinates), weights and exposure protection used, divemasters and dive buddies, etc.

**Viking**— GTK+2 application to manage GPS data.

#### Meteorology

**Gis Weather**— Customizable weather forecast desktop widget.

**GNOME Weather**— Small application for GNOME that allows you to monitor the current weather conditions for your city, or anywhere in the world, and to access updated forecasts provided by various internet services.

**meteo-qt**— System tray application for weather status information.

**wttr**— A simple console application to check the weather, using data from http://wttr.in

**Xfce Weather Panel Plugin**— Weather forecast plugin for the Xfce4 panel.

### 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.

**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.

- https://www.ap-i.net/skychart/ || 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.

**Where Is M13**— Application to visualize the locations and physical properties of deep sky objects.

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

### Biology

**Gramps**— Genealogy program, which helps you track your family tree.

#### Computational biology and bioinformatics

See also Wikipedia:List of open source bioinformatics software.

**BALL (Biochemical Algorithms Library)**— Application framework in C++ that provides an extensive set of data structures as well as classes for molecular mechanics, 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 || biojava
^{AUR}

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

**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/ || not packaged? search in AUR

**MUMmer**— Bioinformatics software system for sequence alignment based on suffix trees.

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

**Snapgene**— Closed source molecular cloning application that offers a fast and easy way to plan, visualize, and document molecular biology procedures. Supports a wide range of cloning and PCR manipulations. The free version allows most common visualizations of a molecular biology workflow.

- http://www.snapgene.com/ || snapgene-viewer
^{AUR}

**UGENE**— Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.

- http://ugene.net/ || ugene-bin
^{AUR}

#### Biochemistry

**Bioclipse**— Java-based visual platform for biochemistry that uses the Eclipse Rich Client Platform (RCP).

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

- https://imagej.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}

#### DICOM viewers and volume rendering

**aeskulap**— Simple DICOM data viewer

- http://www.nongnu.org/aeskulap/ || aeskulap
^{AUR}

**weasis**— Multipurpose DICOM viewer with a highly modular architecture

- https://nroduit.github.io/en/ || weasis-bin
^{AUR}

**aliza**— Open 2D, 3D and 4D images in DICOM, MetaIO, Nifti, Nrrd and other formats, meshes in DICOM, VTK, STL and OBJ formats

- https://www.aliza-dicom-viewer.com/ || aliza
^{AUR}

**Ginkgo CADx**— Advanced DICOM viewer and dicomizer. Continuation of the now abandoned free version developed by MetaEmotion

**3DSlicer**— Comprehensive MRI, CT, LSCM microscopy volume processing, segmentation and 3D-reconstruction

- https://www.slicer.org/ || 3dslicer
^{AUR}

### Engineering

#### Computer-aided design

See also Wikipedia:List of computer-aided design editors.

**BRL-CAD**— Constructive solid geometry (CSG) solid modeling computer-aided design (CAD) system that includes an interactive geometry editor, ray tracing support for graphics rendering and geometric analysis, computer network distributed framebuffer support, scripting, image-processing and signal-processing tools.

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

**DraftSight**— Dassault Systemes' freeware 2D CAD application. DraftSight allows users to access DWG/DXF files, regardless of which CAD software was originally used to create them.

**FreeCAD**— CAD/CAE program, based on OpenCascade, Qt and Python with features such as macro recording, workbenches and the ability to run as server.

**LeoCAD**— CAD program for creating virtual LEGO models. It has an easy to use interface and currently includes over 6000 different pieces created by the LDraw community.

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

**LibreCAD**— Powerful 2D CAD application based on Qt. It has been forked from QCad Community Edition.

**OpenSCAD**— Open source 2D/3D CAD using programmers approach.

**QCAD**— Powerful 2D CAD application that began in 1999. QCaD includes DFX standard file format and supports HPGL format.

#### Electronics

See also Wikipedia:Comparison of EDA software.

##### Digital logic

Digital logic software are mainly simple educational tools that intended for only designing and simulating logic circuits.

**glogic**— An educational graphical logic circuit simulator, written in Python.

- https://launchpad.net/glogic || glogic
^{AUR}

**GTKWave**— Fully featured GTK+ based wave viewer which reads LXT, LXT2, VZT, FST, and GHW files as well as standard Verilog VCD/EVCD files and allows their viewing.

**Logisim**— Educational digital logic design and simulation software, written in Java, officially its development has stopped.

**Logisim Evolution**— Project which continue the development of the original Logisim with new features, written in Java.

**PulseView**— Logic analyzer, oscilloscope and MSO GUI.

**SmartSim**— Simple and beautiful digital logic circuit design and simulation software, mainly target teachers and students, very lightweight and cross platform, GPL licensed, written in Vala.

- https://smartsim.org.uk || smartsim-git
^{AUR}

##### HDL

Also see Wikipedia:Hardware description language.

**Altera Design Software**— A set of design tools for Altera's FPGA chips that includes Quartus II and ModelSim-Altera.

**Xilinx ISE WebPACK**— FPGA programmable logic design suit.

- http://www.xilinx.com/products/design-tools/ise-design-suite/ise-webpack.html || see Xilinx ISE WebPACK

##### MCU IDE

**Arduino**— Arduino prototyping platform SDK.

##### Schematic capture editor

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

**gEDA PCB**— Interactive printed circuit board editor.

**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).

**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/drahnr/oregano || oregano
^{AUR}

**QElectroTech**— Application used to draw advanced electrical circuits.

- https://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
^{AUR}

### Telecommunication

**CupCarbon**— A Smart City & IoT Wireless Sensor Network Simulator.

- http://cupcarbon.com/ || not packaged? search in AUR

**GNU Radio**— Software development toolkit that provides signal processing blocks to implement software radios.

**Gqrx**— Software defined radio receiver implemented using GNU Radio and the Qt GUI toolkit.

**Pothos**— The Pothos project is a complete data-flow framework for creating topologies of interconnected processing blocks.

- https://github.com/pothosware/PothosCore/wiki || pothos
^{AUR}, pothos-git^{AUR}

#### Amateur radio

See the main article: Amateur radio#Software list.

See also Wikipedia:List of software-defined radios.

### Simulation modeling

**gephi**— Gephi is an open-source network analysis and visualization software package written in Java.

**golly**— Golly is an open source, cross-platform application for exploring Conway's Game of Life and many other types of cellular automata.

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

**Netlogo**— NetLogo is a multi-agent programmable modeling environment.

**AnyLogic**— AnyLogic is a cross-platform proprietary multimethod simulation modeling tool, which is also available for personal use.

- https://www.anylogic.com/ || anylogic-ple
^{AUR}, anylogic-university^{AUR}, anylogic-professional^{AUR}

### Computer science

#### Artificial intelligence

See also Wikipedia:Comparison of deep learning software.

**Fast Artificial Neural Network**— Library for developing feedforward Artificial Neural Networks.

- http://leenissen.dk/fann/wp/ || fann
^{AUR}

**Mycroft**— Intelligent personal assistant and knowledge navigator with speech recognition.

- https://mycroft.ai/ || mycroft-core
^{AUR}

**Orange**— Data visualization, machine learning and data mining toolkit, accessible via visual programming and Python.

- https://orange.biolab.si/ || python-orange
^{AUR}

**Torch**— Machine learning library, scientific computing framework, and script language based on LuaJIT.

- http://torch.ch/ || torch7-git
^{AUR}

**X Neural Switcher**— Automatic (intelligent) keyboard layout adaption.

- https://xneur.ru/ || xneur
^{AUR}, gxneur^{AUR}

**Tensorflow**— An end-to-end open source machine learning platform.

- https://www.tensorflow.org/ || python-tensorflow, with CPU optimization python-tensorflow-opt, with CUDA python-tensorflow-cuda, with CUDA and CPU optimizations python-tensorflow-opt-cuda