Difference between revisions of "List of applications/Science"

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[[Category:Mathematics and science]]
 
[[Category:Mathematics and science]]
 
[[Category:Applications]]
 
[[Category:Applications]]
[[it:List of Applications/Science]]
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[[es:List of applications/Science]]
[[ja:List of Applications/Science]]
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[[it:List of applications/Science]]
[[zh-CN:List of Applications/Science]]
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[[ja:アプリケーション一覧/サイエンス]]
{{List of Applications navigation}}
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[[ru:List of applications/Science]]
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[[uk:List of applications/Science]]
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[[zh-cn:List of applications/Science]]
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[[zh-tw:List of applications/Science]]
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{{List of applications navigation}}
 
</noinclude>
 
</noinclude>
 
 
== Science ==
 
== Science ==
  
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=== Scientific documents ===
 
=== Scientific documents ===
  
{{Box||See the main article: [[List of Applications/Documents#Scientific Documents]]|#E5E5FF|#FCFCFC}}
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See the main article: [[List of applications/Documents#Scientific documents]].
  
 
=== Mathematics ===
 
=== Mathematics ===
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==== Calculator ====
 
==== Calculator ====
  
{{Wikipedia|Comparison of software calculators}}
+
See also [[Wikipedia:Comparison of software calculators]].
  
 
* {{App|[[Wikipedia:bc programming language|bc]]|Arbitrary precision calculator language.|http://www.gnu.org/software/bc/|{{Pkg|bc}}}}
 
* {{App|[[Wikipedia:bc programming language|bc]]|Arbitrary precision calculator language.|http://www.gnu.org/software/bc/|{{Pkg|bc}}}}
 
* {{App|calc|Arbitrary precision console calculator.|http://www.isthe.com/chongo/tech/comp/calc/|{{Pkg|calc}}}}
 
* {{App|calc|Arbitrary precision console calculator.|http://www.isthe.com/chongo/tech/comp/calc/|{{Pkg|calc}}}}
 
* {{App|Extcalc|Qt-based scientfic graphical calculator.|http://extcalc-linux.sourceforge.net/|{{AUR|extcalc}}}}
 
* {{App|Extcalc|Qt-based scientfic graphical calculator.|http://extcalc-linux.sourceforge.net/|{{AUR|extcalc}}}}
* {{App|[[Wikipedia:GCalctool|GCalctool]]|Scientific calculator included in the GNOME desktop.|http://www.gnome.org|{{AUR|gcalctool-oldgui}}}}
+
* {{App|galculator|GTK+ based scientific calculator.|http://galculator.sourceforge.net/|{{Pkg|galculator}} {{pkg|galculator-gtk2}}}}
* {{App|KAlgebra|Calculator and 3D plotter included in KDE EDU.|http://www.kde.org/applications/education/kalgebra/|{{Pkg|kdeedu-kalgebra}}}}
+
* {{App|[[Wikipedia:GNOME Calculator|GNOME Calculator]]|Scientific calculator included in the GNOME desktop.|https://wiki.gnome.org/Apps/Calculator|{{Pkg|gnome-calculator}}}}
* {{App|[[Wikipedia:KCalc|KCalc]]|Scientific calculator included in the KDE desktop.|http://kde.org/applications/utilities/kcalc/|{{Pkg|kdeutils-kcalc}}}}
+
* {{App|[[Wikipedia:GNOME Calculator|GCalctool]]|Scientific calculator included in the GNOME desktop (old GTK2 version).|http://www.gnome.org|{{AUR|gcalctool-oldgui}}}}
* {{App|Qalculate|Calculator and equation solver with fault-tolerant parsing, constant recognition and units.|http://qalculate.sourceforge.net/|{{Pkg|libqalculate}}}}
+
* {{App|KAlgebra|Calculator and 3D plotter included in KDE EDU.|http://www.kde.org/applications/education/kalgebra/|{{Pkg|kalgebra}}}}
* {{App|SpeedCrunch|Fast, high precision and powerful cross-platform calculator.|http://speedcrunch.org|{{AUR|speedcrunch}}}}
+
* {{App|[[Wikipedia:KCalc|KCalc]]|Scientific calculator included in the KDE desktop.|http://kde.org/applications/utilities/kcalc/|{{Pkg|kcalc}}}}
 +
* {{App|Qalculate|Calculator and equation solver with fault-tolerant parsing, constant recognition and units.|http://qalculate.github.io/|{{Pkg|libqalculate}}}}
 +
* {{App|SpeedCrunch|Fast, high precision and powerful cross-platform calculator.|http://speedcrunch.org|{{Pkg|speedcrunch}}}}
 
* {{App|[[Wikipedia:xcalc|xcalc]]|Scientific calculator for X with algebraic and reverse polish notation modes.|http://xorg.freedesktop.org/|{{Pkg|xorg-xcalc}}}}
 
* {{App|[[Wikipedia:xcalc|xcalc]]|Scientific calculator for X with algebraic and reverse polish notation modes.|http://xorg.freedesktop.org/|{{Pkg|xorg-xcalc}}}}
  
 
==== Computer algebra system ====
 
==== Computer algebra system ====
  
{{Wikipedia|Comparison of computer algebra systems}}
+
See also [[Wikipedia:Comparison of computer algebra systems]].
  
* {{App|[[Wikipedia:Fermat (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/|{{AUR|fermat}}}}
+
* {{App|[[Wikipedia:Axiom (computer algebra system)|AXIOM]]|FriCAS: derivative of the powerful AXIOM-CAS|http://fricas.sourceforge.net|{{AUR|fricas}}}}
* {{App|[[Wikipedia:GAP (computer algebra system)|GAP]]|Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.|http://www.gap-system.org|{{AUR|gap-math}}}}
+
* {{App|[[Wikipedia:Fermat (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/|{{AUR|fermat}}{{Broken package link|{{aur-mirror|fermat}}}}}}
 +
* {{App|[[Wikipedia:GAP (computer algebra system)|GAP]]|Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.|http://www.gap-system.org|{{Pkg|gap}}}}
 +
* {{App|[[Maple]]|Famous commercial CAS. Often used in education.|http://www.maplesoft.com/products/maple/|}}
 +
* {{App|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/|{{AUR|mathics}}}}  
 
* {{App|[[Wikipedia:Mathomatic|Mathomatic]]|General purpose Computer Algebra System written in C.|http://www.mathomatic.org/|{{Pkg|mathomatic}}}}
 
* {{App|[[Wikipedia:Mathomatic|Mathomatic]]|General purpose Computer Algebra System written in C.|http://www.mathomatic.org/|{{Pkg|mathomatic}}}}
 
* {{App|[[Wikipedia:Maxima (software)|Maxima]]|[[Wikipedia:Maple (software)|Maple]]/[[Wikipedia:Wolfram Mathematica|Mathematica]]-like program with a wxWidgets based frontend.|http://maxima.sourceforge.net/|{{Pkg|maxima}} {{Pkg|wxmaxima}}}}
 
* {{App|[[Wikipedia:Maxima (software)|Maxima]]|[[Wikipedia:Maple (software)|Maple]]/[[Wikipedia:Wolfram Mathematica|Mathematica]]-like program with a wxWidgets based frontend.|http://maxima.sourceforge.net/|{{Pkg|maxima}} {{Pkg|wxmaxima}}}}
 
* {{App|[[Wikipedia:PARI/GP|PARI/GP]]|Computer algebra system designed for fast computations in number theory.|http://pari.math.u-bordeaux.fr/|{{Pkg|pari}}}}
 
* {{App|[[Wikipedia:PARI/GP|PARI/GP]]|Computer algebra system designed for fast computations in number theory.|http://pari.math.u-bordeaux.fr/|{{Pkg|pari}}}}
* {{App|[[Wikipedia:Xcas|Xcas]]|User interface to Giac, a free, basic computer algebra system.|http://www-fourier.ujf-grenoble.fr/~parisse/giac.html|{{AUR|xcas}}}}
+
* {{App|[[Wikipedia:Xcas|Xcas]]|User interface to Giac, a free, basic computer algebra system.|http://www-fourier.ujf-grenoble.fr/~parisse/giac.html|{{Pkg|xcas}}}}
  
 
==== Scientific or technical computing ====
 
==== Scientific or technical computing ====
  
{{Wikipedia|Comparison of numerical analysis software}}
+
See also [[Wikipedia:Comparison of numerical analysis software]].
  
 
* {{App|EngLab|Cross-compile mathematical platform with a C like syntax.|http://englab.bugfest.net|{{AUR|englab}}}}
 
* {{App|EngLab|Cross-compile mathematical platform with a C like syntax.|http://englab.bugfest.net|{{AUR|englab}}}}
* {{App|[[Wikipedia:Euler (software)|Euler]]|Numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.|http://euler.sourceforge.net|{{AUR|euler}}}}
 
 
* {{App|[[Wikipedia:FreeMat|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/|{{Pkg|freemat}}}}
 
* {{App|[[Wikipedia:FreeMat|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/|{{Pkg|freemat}}}}
 +
* {{App|[[GNU Radio]]|Software development toolkit that provides signal processing blocks to implement software radios.|http://gnuradio.org/redmine/projects/gnuradio/wiki |{{Pkg|gnuradio}}}}
 +
* {{App|[[Wikipedia:matplotlib|matplotlib (PyLab)]]|Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.|http://www.scipy.org/|{{Pkg|python-matplotlib}}}}
 
* {{App|[[Octave]]|[[Matlab]]-like language and interface for numerical computations.|http://www.gnu.org/software/octave/ |{{Pkg|octave}}}}
 
* {{App|[[Octave]]|[[Matlab]]-like language and interface for numerical computations.|http://www.gnu.org/software/octave/ |{{Pkg|octave}}}}
* {{App|[[Wikipedia:matplotlib|PyLab]]|Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.|http://www.scipy.org/PyLab|{{Pkg|python2-matplotlib}}}}
+
* {{App|[[Sage-mathematics]]|Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.|http://www.sagemath.org|{{Pkg|sagemath}}}}
* {{App|[[Sage]]|Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.|http://www.sagemath.org|{{Pkg|sage-mathematics}}}}
+
 
* {{App|[[Wikipedia:Scilab|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/|{{AUR|scilab}}}}
 
* {{App|[[Wikipedia:Scilab|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/|{{AUR|scilab}}}}
  
 
==== Statistics ====
 
==== Statistics ====
  
{{Wikipedia|Comparison of statistical packages}}
+
See also [[Wikipedia:Comparison of statistical packages]].
  
 
* {{App|[[Wikipedia:Just another Gibbs sampler|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/|{{AUR|jags}}}}
 
* {{App|[[Wikipedia:Just another Gibbs sampler|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/|{{AUR|jags}}}}
 +
* {{App|[[Wikipedia:Pandas_(software)|Python Data Analysis Library (pandas)]]| Providing high-performance, easy-to-use data structures and data analysis tools with Python programming language.|http://pandas.pydata.org/|{{Pkg|python2-pandas}} {{Pkg|python-pandas}}}}
 
* {{App|[[Wikipedia:PSPP|PSPP]]|Free SPSS implementation.|http://www.gnu.org/software/pspp/|{{AUR|pspp}}}}
 
* {{App|[[Wikipedia:PSPP|PSPP]]|Free SPSS implementation.|http://www.gnu.org/software/pspp/|{{AUR|pspp}}}}
 
* {{App|[[R]]|Software environment for statistical computing and graphics.|http://cran.r-project.org/|{{Pkg|r}}}}
 
* {{App|[[R]]|Software environment for statistical computing and graphics.|http://cran.r-project.org/|{{Pkg|r}}}}
 
* {{App|[[Wikipedia:RKWard|RKWard]]|Frontend for the statistical language R.|http://rkward.sourceforge.net/|{{AUR|rkward}}}}
 
* {{App|[[Wikipedia:RKWard|RKWard]]|Frontend for the statistical language R.|http://rkward.sourceforge.net/|{{AUR|rkward}}}}
 +
* {{App|[[Wikipedia:RStudio|RStudio]]|A powerful and productive IDE for R written in Qt.|http://www.rstudio.com/|{{AUR|rstudio-desktop-bin}}}}
  
 
==== Data evaluation ====
 
==== Data evaluation ====
  
{{Wikipedia|List of information graphics software}}
+
See also [[Wikipedia:List of information graphics software]].
  
* {{App|Extrema|Visualization and data analysis tool.|http://sourceforge.net/projects/extrema|{{AUR|extrema}}}}
 
 
* {{App|[[Wikipedia:Fityk|Fityk]]|Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.|http://fityk.nieto.pl/|{{AUR|fityk}}}}
 
* {{App|[[Wikipedia:Fityk|Fityk]]|Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.|http://fityk.nieto.pl/|{{AUR|fityk}}}}
 
* {{App|[[Wikipedia:gnuplot|Gnuplot]]|Command-line program that can generate 2D and 3D plots of functions, data, and data fits. |http://www.gnuplot.info/|{{Pkg|gnuplot}}}}
 
* {{App|[[Wikipedia:gnuplot|Gnuplot]]|Command-line program that can generate 2D and 3D plots of functions, data, and data fits. |http://www.gnuplot.info/|{{Pkg|gnuplot}}}}
 
* {{App|[[Wikipedia:Grace (plotting tool)|Grace]]|WYSIWYG 2D graph plotting tool.|http://plasma-gate.weizmann.ac.il/Grace/|{{Pkg|grace}} {{AUR|qtgrace}} {{AUR|gracegtk}}}}
 
* {{App|[[Wikipedia:Grace (plotting tool)|Grace]]|WYSIWYG 2D graph plotting tool.|http://plasma-gate.weizmann.ac.il/Grace/|{{Pkg|grace}} {{AUR|qtgrace}} {{AUR|gracegtk}}}}
* {{App|[[Wikipedia:LabPlot|LabPlot]]|Free software data analysis and visualization application, similar to SciDAVis.|http://labplot.sourceforge.net/|{{AUR|labplot2}}}}
+
* {{App|[[Wikipedia:LabPlot|LabPlot]]|Free software data analysis and visualization application, similar to SciDAVis.|https://labplot.kde.org/|{{AUR|labplot-kf5}}}}
* {{App|[[Wikipedia:QtiPlot|QtiPlot]]|Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary [[Wikipedia: Origin (software)|Origin]] or [[Wikipedia:SigmaPlot|SigmaPlot]].|http://soft.proindependent.com/qtiplot.html|{{Pkg|qtiplot}}}}
+
* {{App|[[Wikipedia:QtiPlot|QtiPlot]]|Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary [[Wikipedia:Origin (software)|Origin]] or [[Wikipedia:SigmaPlot|SigmaPlot]].|http://www.qtiplot.com/|{{Pkg|qtiplot}}}}
 
* {{App|[[Wikipedia:ROOT|ROOT]]|Data analysis program and library (originally for particle physics) developed by CERN.|http://root.cern.ch/drupal/|{{AUR|root}}}}
 
* {{App|[[Wikipedia:ROOT|ROOT]]|Data analysis program and library (originally for particle physics) developed by CERN.|http://root.cern.ch/drupal/|{{AUR|root}}}}
 
* {{App|[[Wikipedia:SciDAVis|SciDAVis]]|Fork of QtiPlot with the goal of being better documented and more user friendly.|http://scidavis.sourceforge.net/|{{AUR|scidavis}}}}
 
* {{App|[[Wikipedia:SciDAVis|SciDAVis]]|Fork of QtiPlot with the goal of being better documented and more user friendly.|http://scidavis.sourceforge.net/|{{AUR|scidavis}}}}
See also [[List of Applications#Spreadsheets]]
+
See also [[List of applications#Spreadsheets]]
  
 
=== Chemistry and biology ===
 
=== Chemistry and biology ===
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====Computational biology and bioinformatics====
 
====Computational biology and bioinformatics====
  
{{Wikipedia|List of open source bioinformatics software}}
+
See also [[Wikipedia:List of open source bioinformatics software]].
  
* {{App|[[Wikipedia:BALL|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/|{{AUR|ball}}}}
+
* {{App|[[Wikipedia:BALL|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/|{{AUR|ball}}}}
* {{App|[[Wikipedia:BioJava|BioJava]]|Set of Java tools for computational biology, as well as bioinformatics.|http://biojava.org/wiki/Main_Page|{{AUR|biojava}}}}
+
* {{App|[[Wikipedia:BioJava|BioJava]]|Set of Java tools for computational biology, as well as bioinformatics.|http://biojava.org|{{AUR|biojava}}}}
* {{App|[[Wikipedia:Biopython|Biopython]]|Python package with tools for computational biology, as well as bioinformatics.|http://biopython.org/wiki/Biopython|{{AUR|python-biopython}} {{AUR|python2-biopython}}}}
+
* {{App|[[Wikipedia:Biopython|Biopython]]|Python package with tools for computational biology, as well as bioinformatics.|http://biopython.org/wiki/Biopython|{{Pkg|python-biopython}} {{Pkg|python2-biopython}}}}
 
* {{App|[[Wikipedia:EMBOSS|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/|{{AUR|emboss}}}}
 
* {{App|[[Wikipedia:EMBOSS|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/|{{AUR|emboss}}}}
* {{App|[[Wikipedia:MEGA, Molecular Evolutionary Genetics Analysis|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/|{{AUR|mega}}}}
+
* {{App|[[Wikipedia:MEGA, Molecular Evolutionary Genetics Analysis|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/}}
 
* {{App|[[Wikipedia:MUMmer|MUMmer]]|Bioinformatics software system for sequence alignment based on suffix trees.|http://mummer.sourceforge.net/|{{AUR|mummer}}}}
 
* {{App|[[Wikipedia:MUMmer|MUMmer]]|Bioinformatics software system for sequence alignment based on suffix trees.|http://mummer.sourceforge.net/|{{AUR|mummer}}}}
 
* {{App|[[Wikipedia:UGENE|UGENE]]|Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.|http://ugene.unipro.ru/|{{AUR|ugene}}}}
 
* {{App|[[Wikipedia:UGENE|UGENE]]|Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.|http://ugene.unipro.ru/|{{AUR|ugene}}}}
  
==== Molecule viewer ====
+
==== Molecules ====
  
{{Wikipedia|List of molecular graphics systems}}
+
===== Viewers =====
 +
 
 +
See also [[Wikipedia:List of molecular graphics systems]].
  
 
* {{App|[[Wikipedia:Avogadro_(software)|Avogadro]]|Editor, viewer and simulator for 3D molecule structures (also supports downloading files from the [[Wikipedia:Protein Data Bank|Protein Data Bank]]).|http://avogadro.openmolecules.net/wiki/Main_Page|{{Pkg|avogadro}}}}
 
* {{App|[[Wikipedia:Avogadro_(software)|Avogadro]]|Editor, viewer and simulator for 3D molecule structures (also supports downloading files from the [[Wikipedia:Protein Data Bank|Protein Data Bank]]).|http://avogadro.openmolecules.net/wiki/Main_Page|{{Pkg|avogadro}}}}
 
* {{App|BALLView|Standalone molecular modeling and visualization application, part of the [[Wikipedia:BALL|BALL]] framework.|http://www.ballview.org/|{{AUR|ball}}}}
 
* {{App|BALLView|Standalone molecular modeling and visualization application, part of the [[Wikipedia:BALL|BALL]] framework.|http://www.ballview.org/|{{AUR|ball}}}}
 
* {{App|[[Wikipedia:Ghemical|Ghemical]]|Computational chemistry software package used to edit, view and simulate molecular structures.|http://bioinformatics.org/ghemical/ghemical/index.html|{{AUR|ghemical}}}}
 
* {{App|[[Wikipedia:Ghemical|Ghemical]]|Computational chemistry software package used to edit, view and simulate molecular structures.|http://bioinformatics.org/ghemical/ghemical/index.html|{{AUR|ghemical}}}}
* {{App|[[Wikipedia:PyMOL|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|{{AUR|pymol}}}}
+
* {{App|[[Wikipedia:PyMOL|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|{{Pkg|pymol}}}}
* {{App|[[Wikipedia:RasMol|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/|{{AUR|rasmol}}}}
+
* {{App|[[Wikipedia:RasMol|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/|{{AUR|rasmol}}{{Broken package link|{{aur-mirror|rasmol}}}}}}
  
==== Molecule drawing ====
+
===== Drawing =====
  
 
* {{App|[[Wikipedia:BKchem|BKChem]]|Practical and goodlooking skeletal formula molecule drawing program.|http://bkchem.zirael.org/|{{AUR|bkchem}}}}
 
* {{App|[[Wikipedia:BKchem|BKChem]]|Practical and goodlooking skeletal formula molecule drawing program.|http://bkchem.zirael.org/|{{AUR|bkchem}}}}
Line 108: Line 119:
 
* {{App|EasyChem|Simple skeletal formula molecule drawing program with a focus on producing press-quality figures.|http://easychem.sourceforge.net/|{{AUR?|easychem}}}}
 
* {{App|EasyChem|Simple skeletal formula molecule drawing program with a focus on producing press-quality figures.|http://easychem.sourceforge.net/|{{AUR?|easychem}}}}
 
* {{App|[[Wikipedia:Gabedit|Gabedit]]|Graphical user interface to computational chemistry packages like [[Wikipedia:GAMESS (US)|GAMESS]], [[Wikipedia:Gaussian (software)|Gaussian]], [[Wikipedia:MOLCAS|MOLCAS]], [[Wikipedia:MOLPRO|MOLPRO]], [[Wikipedia:MPQC|MPQC]], [[Wikipedia:MOPAC|OpenMopac]], [[Wikipedia:PC GAMESS|Firefly]] (previously PC GAMESS) and [[Wikipedia:Q-Chem|Q-Chem]].|http://gabedit.sourceforge.net/|{{AUR|gabedit}}}}
 
* {{App|[[Wikipedia:Gabedit|Gabedit]]|Graphical user interface to computational chemistry packages like [[Wikipedia:GAMESS (US)|GAMESS]], [[Wikipedia:Gaussian (software)|Gaussian]], [[Wikipedia:MOLCAS|MOLCAS]], [[Wikipedia:MOLPRO|MOLPRO]], [[Wikipedia:MPQC|MPQC]], [[Wikipedia:MOPAC|OpenMopac]], [[Wikipedia:PC GAMESS|Firefly]] (previously PC GAMESS) and [[Wikipedia:Q-Chem|Q-Chem]].|http://gabedit.sourceforge.net/|{{AUR|gabedit}}}}
* {{App|[[Wikipedia:XDrawChem|XDrawChem]]|Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).|http://xdrawchem.sourceforge.net/|{{AUR|xdrawchem}}}}
+
 
 +
===== Modeling =====
 +
 
 +
* {{App|[[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|{{AUR|gromacs}}}}
 +
* {{App|[[Wikipedia:Quantum ESPRESSO|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).|http://www.quantum-espresso.org/|{{AUR|quantum-espresso}}}}
  
 
==== Periodic table ====
 
==== Periodic table ====
  
 +
* {{App|eperiodique|A simple Periodic Table Of Elements viewer using the EFL.|http://eperiodique.sourceforge.net/|{{AUR|eperiodique}}}}
 
* {{App|gElemental|Periodic table of the elements with additional information.|http://freshmeat.net/projects/gelemental|{{AUR|gelemental}}}}
 
* {{App|gElemental|Periodic table of the elements with additional information.|http://freshmeat.net/projects/gelemental|{{AUR|gelemental}}}}
 
* {{App|[[Wikipedia:Kalzium|Kalzium]]|Periodic table of the elements with molecule editor and equation solver from the [[KDE]] desktop.|http://edu.kde.org/kalzium/|{{Pkg|kdeedu-kalzium}}}}
 
* {{App|[[Wikipedia:Kalzium|Kalzium]]|Periodic table of the elements with molecule editor and equation solver from the [[KDE]] desktop.|http://edu.kde.org/kalzium/|{{Pkg|kdeedu-kalzium}}}}
Line 117: Line 133:
 
==== Biochemistry ====
 
==== Biochemistry ====
  
* {{App|[[Wikipedia:Bioclipse|Bioclipse]]|Java-based visual platform for biochemestry that uses the Eclipse Rich Client Platform (RCP).|http://www.bioclipse.net/|{{AUR?|bioclipse}}}}
+
* {{App|[[Wikipedia:Bioclipse|Bioclipse]]|Java-based visual platform for biochemistry that uses the Eclipse Rich Client Platform (RCP).|http://www.bioclipse.net/|{{AUR?|bioclipse}}}}
 
+
==== Molecular modeling ====
+
 
+
* {{App|[[Wikipedia:GROMACS|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|{{AUR|gromacs}}}}
+
* {{App|[[Wikipedia:Quantum ESPRESSO|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).|http://www.quantum-espresso.org/|{{AUR|quantum-espresso}}}}
+
  
 
==== Image manipulation ====
 
==== Image manipulation ====
  
 
* {{App|[[Wikipedia:ImageJ|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|{{AUR|imagej}}}}
 
* {{App|[[Wikipedia:ImageJ|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|{{AUR|imagej}}}}
 +
* {{App|[[Wikipedia:FIJI_(software)|Fiji]]|ImageJ distribution (and soon ImageJ2) with a lot of plugins organized into a coherent menu structure.|http://fiji.sc|{{AUR|fiji-binary}}}}
  
 
=== Astronomy ===
 
=== Astronomy ===
Line 133: Line 145:
 
* {{App|GIMP Astronomy Plugins|Set of GIMP plugins for astronomical image processing.|http://hennigbuam.de/georg/gimp.html|{{AUR|gimp-plugin-astronomy}}}}
 
* {{App|GIMP Astronomy Plugins|Set of GIMP plugins for astronomical image processing.|http://hennigbuam.de/georg/gimp.html|{{AUR|gimp-plugin-astronomy}}}}
 
* {{App|GoQat|Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.|http://canburytech.net/GoQat/|{{AUR|goqat}}}}
 
* {{App|GoQat|Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.|http://canburytech.net/GoQat/|{{AUR|goqat}}}}
* {{App|[[Wikipedia:KStars|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.|http://edu.kde.org/kstars/|{{Pkg|kdeedu-kstars}}}}
+
* {{App|[[Wikipedia:KStars|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.|http://edu.kde.org/kstars/|{{Pkg|kstars}}}}
* {{App|Open PHD Guiding|Telescope autoguiding software based on the famous PHD Guiding.|http://code.google.com/p/open-phd-guiding/|{{AUR|open-phd-guiding-svn}}}}
+
* {{App|Open PHD Guiding|Telescope autoguiding software based on the famous PHD Guiding.|http://openphdguiding.org/|{{AUR|open-phd-guiding-svn}}{{Broken package link|{{aur-mirror|open-phd-guiding-svn}}}}}}
 
* {{App|Qastrocam-g2|Webcam acquisition software for planetary imaging.|http://sourceforge.net/projects/qastrocam-g2/|{{AUR|qastrocam-g2}}}}
 
* {{App|Qastrocam-g2|Webcam acquisition software for planetary imaging.|http://sourceforge.net/projects/qastrocam-g2/|{{AUR|qastrocam-g2}}}}
 
* {{App|[[Wikipedia:Cartes du Ciel|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.|http://www.ap-i.net/skychart/start/|{{AUR|skychart}}}}
 
* {{App|[[Wikipedia:Cartes du Ciel|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.|http://www.ap-i.net/skychart/start/|{{AUR|skychart}}}}
 
* {{App|StarPlot|3-dimensional star chart viewer.|http://starplot.org/|{{AUR|starplot}}}}
 
* {{App|StarPlot|3-dimensional star chart viewer.|http://starplot.org/|{{AUR|starplot}}}}
 
* {{App|[[Wikipedia:Stellarium (computer program)|Stellarium]]|Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.|http://www.stellarium.org/|{{Pkg|stellarium}}}}
 
* {{App|[[Wikipedia:Stellarium (computer program)|Stellarium]]|Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.|http://www.stellarium.org/|{{Pkg|stellarium}}}}
 +
* {{App|Where Is M13|Application to visualize the locations and physical properties of deep sky objects.|http://www.thinkastronomy.com/M13/|{{AUR|where-is-m13}}}}
 
* {{App|[[Wikipedia:XEphem|XEphem]]|Motif-based ephemeris and planetarium program.|http://www.clearskyinstitute.com/xephem/xephem.html|{{AUR|xephem}}}}
 
* {{App|[[Wikipedia:XEphem|XEphem]]|Motif-based ephemeris and planetarium program.|http://www.clearskyinstitute.com/xephem/xephem.html|{{AUR|xephem}}}}
  
Line 145: Line 158:
 
==== Electronics ====
 
==== Electronics ====
  
{{Wikipedia|Comparison of EDA software}}
+
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.
 +
 
 +
* {{App|glogic|An educational graphical logic circuit simulator.|https://launchpad.net/glogic|{{AUR|glogic}}}}
 +
* {{App|Logisim|Educational digital logic design and simulation software, written in Java, officially its development has stopped.|http://sourceforge.net/projects/circuit/|{{AUR|logisim}}}}
 +
* {{App|Logisim Evolution|Project which continue the development of the original Logisim with new features, written in Java.|https://github.com/reds-heig/logisim-evolution|{{AUR|logisim-evolution-git}}}}
 +
* {{App|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.|http://smartsim.org.uk|{{AUR|smartsim-git}}}}
 +
 
 +
===== HDL =====
 +
 
 +
* {{App|[[Altera Design Software]]|A set of design tools for Altera's FPGA chips that includes Quartus II and ModelSim-Altera.|http://www.altera.com/products/software/sfw-index.jsp|see [[Altera Design Software]]}}
 +
* {{App|[[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 =====
 +
 
 +
* {{App|[[Arduino]]|Arduino prototyping platform SDK.|http://arduino.cc/en/Main/Software|{{AUR|arduino}}}}
 +
 
 +
===== Schematic capture editor =====
  
 
* {{App|[[gEDA]]|Full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.|http://www.geda-project.org/|{{Pkg|geda-gaf}}}}
 
* {{App|[[gEDA]]|Full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.|http://www.geda-project.org/|{{Pkg|geda-gaf}}}}
 
* {{App|[[Wikipedia:KiCAD|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).|http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite|{{Pkg|kicad}}}}
 
* {{App|[[Wikipedia:KiCAD|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).|http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite|{{Pkg|kicad}}}}
* {{App|KLogic|Application used for easily building and simulating digital circuits.|http://www.a-rostin.de/|{{AUR|klogic}}}}
+
* {{App|[[Wikipedia:Oregano (software)|Oregano]]|Graphical software application for schematic capture and simulation of electrical circuits. The actual simulation is done by the [[Wikipedia:Ngspice|ngspice]] or [[Wikipedia:GNU Circuit Analysis Package|Gnucap]] engines.|https://github.com/drahnr/oregano|{{AUR|oregano}}}}
* {{App|[[Wikipedia:KTechLab|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.|http://sourceforge.net/projects/ktechlab/|{{Pkg|ktechlab}}}}
+
* {{App|[[Wikipedia:Oregano (software)|Oregano]]|Graphical software application for schematic capture and simulation of electrical circuits. The actual simulation is done by the [[Wikipedia:Ngspice|ngspice]] or [[Wikipedia:GNU Circuit Analysis Package|Gnucap]] engines.|https://github.com/marc-lorber/oregano|{{AUR|oregano}}}}
+
 
* {{App|QElectroTech|Application used to draw advanced electrical circuits.|http://qelectrotech.org/|{{AUR|qelectrotech}}}}
 
* {{App|QElectroTech|Application used to draw advanced electrical circuits.|http://qelectrotech.org/|{{AUR|qelectrotech}}}}
 
* {{App|[[Wikipedia:Quite Universal Circuit Simulator|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/|{{Pkg|qucs}}}}
 
* {{App|[[Wikipedia:Quite Universal Circuit Simulator|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/|{{Pkg|qucs}}}}
Line 157: Line 188:
 
==== Physics simulation ====
 
==== Physics simulation ====
  
* {{App|[[Wikipedia:Code_Aster|Code_Aster]]|Software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.|http://www.code-aster.org|{{AUR|aster}}}}
+
* {{App|[[Wikipedia:Code_Aster|Code_Aster]]|Software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.|http://www.code-aster.org/V2/spip.php?rubrique2|{{AUR|aster}}}}
* {{App|[[Wikipedia:Step (software)|Step]]|Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.|http://edu.kde.org/step/|{{Pkg|kdeedu-step}}}}
+
* {{App|[[Wikipedia:EPANET|EPANET]]|EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.|http://www.epa.gov/|{{AUR|epanet2-git}}}}
 +
* {{App|[[Wikipedia:Step (software)|Step]]|Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.|http://edu.kde.org/step/|{{Pkg|step}}}}
 +
* {{App|[[Wikipedia:SWMM|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/|{{AUR|swmm5-git}}}}
  
 
==== Unit conversion ====
 
==== Unit conversion ====
Line 165: Line 198:
 
* {{App|Gonvert|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|Gonvert|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|[[Wikipedia:GNU Units|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.|http://www.gnu.org/s/units/|{{Pkg|units}}}}
 
* {{App|[[Wikipedia:GNU Units|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.|http://www.gnu.org/s/units/|{{Pkg|units}}}}
 +
 +
=== Geography ===
 +
 +
* {{App|GNOME Maps|A simple map client for GNOME. Part of {{Grp|gnome-extra}}.|https://wiki.gnome.org/Apps/Maps|{{Pkg|gnome-maps}}}}
 +
* {{App|JOSM|An editor for OpenStreetMap written in Java.|http://josm.openstreetmap.de/|{{Pkg|josm}}}}
 +
* {{App|Marble|Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of {{Grp|kdeedu}}.|https://www.kde.org/applications/education/marble|{{Pkg|marble}}}}
 +
* {{App|Merkaartor|OpenStreetMap editor.|http://merkaartor.be/|{{Pkg|merkaartor}}}}
 +
* {{App|Viking|GTK+2 application to manage GPS data.|http://viking.sourceforge.net/|{{Pkg|viking}}}}

Latest revision as of 17:52, 24 October 2016

Science

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

Scientific documents

See the main article: List of applications/Documents#Scientific documents.

Mathematics

Calculator

See also Wikipedia:Comparison of software calculators.

  • bc — Arbitrary precision calculator language.
http://www.gnu.org/software/bc/ || bc
  • calc — Arbitrary precision console calculator.
http://www.isthe.com/chongo/tech/comp/calc/ || calc
  • Extcalc — Qt-based scientfic graphical calculator.
http://extcalc-linux.sourceforge.net/ || extcalcAUR
  • galculator — GTK+ based scientific calculator.
http://galculator.sourceforge.net/ || galculator galculator-gtk2
https://wiki.gnome.org/Apps/Calculator || gnome-calculator
  • GCalctool — Scientific calculator included in the GNOME desktop (old GTK2 version).
http://www.gnome.org || gcalctool-oldguiAUR
  • KAlgebra — Calculator and 3D plotter included in KDE EDU.
http://www.kde.org/applications/education/kalgebra/ || kalgebra
  • KCalc — Scientific calculator included in the KDE desktop.
http://kde.org/applications/utilities/kcalc/ || kcalc
  • Qalculate — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.
http://qalculate.github.io/ || libqalculate
  • SpeedCrunch — Fast, high precision and powerful cross-platform calculator.
http://speedcrunch.org || speedcrunch
  • xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.
http://xorg.freedesktop.org/ || xorg-xcalc

Computer algebra system

See also Wikipedia:Comparison of computer algebra systems.

  • AXIOM — FriCAS: derivative of the powerful AXIOM-CAS
http://fricas.sourceforge.net || fricasAUR
  • 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/ || fermatAUR[broken link: archived in aur-mirror]
  • GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.
http://www.gap-system.org || gap
  • Maple — Famous commercial CAS. Often used in education.
http://www.maplesoft.com/products/maple/ ||
  • 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/ || mathicsAUR
  • Mathomatic — General purpose Computer Algebra System written in C.
http://www.mathomatic.org/ || mathomatic
http://maxima.sourceforge.net/ || maxima wxmaxima
  • PARI/GP — Computer algebra system designed for fast computations in number theory.
http://pari.math.u-bordeaux.fr/ || pari
  • Xcas — User interface to Giac, a free, basic computer algebra system.
http://www-fourier.ujf-grenoble.fr/~parisse/giac.html || xcas

Scientific or technical computing

See also Wikipedia:Comparison of numerical analysis software.

  • EngLab — Cross-compile mathematical platform with a C like syntax.
http://englab.bugfest.net || englabAUR
  • 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
  • GNU Radio — Software development toolkit that provides signal processing blocks to implement software radios.
http://gnuradio.org/redmine/projects/gnuradio/wiki || gnuradio
  • matplotlib (PyLab) — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
http://www.scipy.org/ || python-matplotlib
  • OctaveMatlab-like language and interface for numerical computations.
http://www.gnu.org/software/octave/ || octave
  • Sage-mathematics — Mathematics software system, that combines many existing open-source packages into a common Python interface. Alternative to Magma, Maple, Mathematica and Matlab.
http://www.sagemath.org || sagemath
  • 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/ || scilabAUR

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/ || jagsAUR
http://pandas.pydata.org/ || python2-pandas python-pandas
  • PSPP — Free SPSS implementation.
http://www.gnu.org/software/pspp/ || psppAUR
  • R — Software environment for statistical computing and graphics.
http://cran.r-project.org/ || r
  • RKWard — Frontend for the statistical language R.
http://rkward.sourceforge.net/ || rkwardAUR
  • RStudio — A powerful and productive IDE for R written in Qt.
http://www.rstudio.com/ || rstudio-desktop-binAUR

Data evaluation

See also Wikipedia:List of information graphics software.

  • Fityk — Curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.
http://fityk.nieto.pl/ || fitykAUR
  • Gnuplot — Command-line program that can generate 2D and 3D plots of functions, data, and data fits.
http://www.gnuplot.info/ || gnuplot
  • Grace — WYSIWYG 2D graph plotting tool.
http://plasma-gate.weizmann.ac.il/Grace/ || grace qtgraceAUR gracegtkAUR
  • LabPlot — Free software data analysis and visualization application, similar to SciDAVis.
https://labplot.kde.org/ || labplot-kf5AUR
  • QtiPlot — Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.
http://www.qtiplot.com/ || qtiplot
  • ROOT — Data analysis program and library (originally for particle physics) developed by CERN.
http://root.cern.ch/drupal/ || rootAUR
  • SciDAVis — Fork of QtiPlot with the goal of being better documented and more user friendly.
http://scidavis.sourceforge.net/ || scidavisAUR

See also List of applications#Spreadsheets

Chemistry and biology

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/ || ballAUR
  • BioJava — Set of Java tools for computational biology, as well as bioinformatics.
http://biojava.org || biojavaAUR
  • Biopython — Python package with tools for computational biology, as well as bioinformatics.
http://biopython.org/wiki/Biopython || python-biopython python2-biopython
  • 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/ || embossAUR
  • 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/ || mummerAUR
  • UGENE — Application that integrates dozens of well-known biological tools and algorithms, providing both graphical user and command-line interfaces.
http://ugene.unipro.ru/ || ugeneAUR

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.openmolecules.net/wiki/Main_Page || avogadro
  • BALLView — Standalone molecular modeling and visualization application, part of the BALL framework.
http://www.ballview.org/ || ballAUR
  • Ghemical — Computational chemistry software package used to edit, view and simulate molecular structures.
http://bioinformatics.org/ghemical/ghemical/index.html || ghemicalAUR
  • 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
  • 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/ || rasmolAUR[broken link: archived in aur-mirror]
Drawing
  • BKChem — Practical and goodlooking skeletal formula molecule drawing program.
http://bkchem.zirael.org/ || bkchemAUR
  • Chemtool — GTK+-based program for drawing chemical structural formulas.
http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html || chemtool
  • EasyChem — Simple skeletal formula molecule drawing program with a focus on producing press-quality figures.
http://easychem.sourceforge.net/ || not packaged? search in AUR
http://gabedit.sourceforge.net/ || gabeditAUR
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 || gromacsAUR
  • 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).
http://www.quantum-espresso.org/ || quantum-espressoAUR

Periodic table

  • eperiodique — A simple Periodic Table Of Elements viewer using the EFL.
http://eperiodique.sourceforge.net/ || eperiodiqueAUR
  • gElemental — Periodic table of the elements with additional information.
http://freshmeat.net/projects/gelemental || gelementalAUR
  • Kalzium — Periodic table of the elements with molecule editor and equation solver from the KDE desktop.
http://edu.kde.org/kalzium/ || kdeedu-kalzium

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).
http://rsb.info.nih.gov/ij || imagejAUR
  • Fiji — ImageJ distribution (and soon ImageJ2) with a lot of plugins organized into a coherent menu structure.
http://fiji.sc || fiji-binaryAUR

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.
http://www.shatters.net/celestia/ || celestia
  • GIMP Astronomy Plugins — Set of GIMP plugins for astronomical image processing.
http://hennigbuam.de/georg/gimp.html || gimp-plugin-astronomyAUR
  • GoQat — Camera acquisition software, especially for QSI cameras, that provides other features such as autoguiding, focusing help and others.
http://canburytech.net/GoQat/ || goqatAUR
  • 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.
http://edu.kde.org/kstars/ || kstars
  • Open PHD Guiding — Telescope autoguiding software based on the famous PHD Guiding.
http://openphdguiding.org/ || open-phd-guiding-svnAUR[broken link: archived in aur-mirror]
  • Qastrocam-g2 — Webcam acquisition software for planetary imaging.
http://sourceforge.net/projects/qastrocam-g2/ || qastrocam-g2AUR
  • 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.
http://www.ap-i.net/skychart/start/ || skychartAUR
  • StarPlot — 3-dimensional star chart viewer.
http://starplot.org/ || starplotAUR
  • Stellarium — Beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.
http://www.stellarium.org/ || stellarium
  • Where Is M13 — Application to visualize the locations and physical properties of deep sky objects.
http://www.thinkastronomy.com/M13/ || where-is-m13AUR
  • XEphem — Motif-based ephemeris and planetarium program.
http://www.clearskyinstitute.com/xephem/xephem.html || xephemAUR

Physics

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.
https://launchpad.net/glogic || glogicAUR
  • Logisim — Educational digital logic design and simulation software, written in Java, officially its development has stopped.
http://sourceforge.net/projects/circuit/ || logisimAUR
  • Logisim Evolution — Project which continue the development of the original Logisim with new features, written in Java.
https://github.com/reds-heig/logisim-evolution || logisim-evolution-gitAUR
  • 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.
http://smartsim.org.uk || smartsim-gitAUR
HDL
  • Altera Design Software — A set of design tools for Altera's FPGA chips that includes Quartus II and ModelSim-Altera.
http://www.altera.com/products/software/sfw-index.jsp || see Altera Design Software
http://www.xilinx.com/products/design-tools/ise-design-suite/ise-webpack.html || see Xilinx ISE WebPACK
MCU IDE
  • Arduino — Arduino prototyping platform SDK.
http://arduino.cc/en/Main/Software || arduinoAUR
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.
http://www.geda-project.org/ || geda-gaf
  • 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).
http://www.kicad-pcb.org/display/KICAD/KiCad+EDA+Software+Suite || kicad
  • 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 || oreganoAUR
  • QElectroTech — Application used to draw advanced electrical circuits.
http://qelectrotech.org/ || qelectrotechAUR
  • 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

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/V2/spip.php?rubrique2 || asterAUR
  • EPANET — EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.
http://www.epa.gov/ || epanet2-gitAUR
  • Step — Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.
http://edu.kde.org/step/ || step
  • 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-gitAUR

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/ || convertallAUR
  • Gonvert — 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/ || gonvertAUR
  • 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.
http://www.gnu.org/s/units/ || units

Geography

  • GNOME Maps — A simple map client for GNOME. Part of gnome-extra.
https://wiki.gnome.org/Apps/Maps || gnome-maps
  • JOSM — An editor for OpenStreetMap written in Java.
http://josm.openstreetmap.de/ || josm
  • Marble — Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of kdeedu.
https://www.kde.org/applications/education/marble || marble
  • Merkaartor — OpenStreetMap editor.
http://merkaartor.be/ || merkaartor
  • Viking — GTK+2 application to manage GPS data.
http://viking.sourceforge.net/ || viking