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 | + | [[es:List of applications/Science]] |
− | [[ja:List of | + | [[it:List of applications/Science]] |
− | [[zh- | + | [[ja:アプリケーション一覧/サイエンス]] |
− | {{List of | + | [[ru:List of applications/Science]] |
+ | [[zh-cn:List of applications/Science]] | ||
+ | [[zh-tw:List of applications/Science]] | ||
+ | {{List of applications navigation}} | ||
</noinclude> | </noinclude> | ||
− | |||
== Science == | == Science == | ||
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=== Scientific documents === | === Scientific documents === | ||
− | + | See the main article: [[List of applications/Documents#Scientific documents]]. | |
=== Mathematics === | === Mathematics === | ||
Line 20: | Line 22: | ||
==== Calculator ==== | ==== Calculator ==== | ||
− | + | 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: | + | * {{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| | + | * {{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| | + | * {{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. | + | * {{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|{{ | + | * {{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 ==== | ||
− | + | 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: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/|{{AUR?|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|{{AUR|xcas}}}} | ||
==== Scientific or technical computing ==== | ==== Scientific or technical computing ==== | ||
− | + | 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: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}}{{Broken package link|{{aur-mirror|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|[[ | + | * {{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|[[Wikipedia:Scilab|Scilab]]|Matlab alternative used for numerical computations | + | * {{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 ==== | ||
− | + | 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/|{{AUR|python2-pandas-git}}}} | ||
* {{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/{{ | + | * {{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 ==== | ||
− | + | See also [[Wikipedia:List of information graphics software]]. | |
− | * {{App|Extrema|Visualization and data analysis tool.|http://sourceforge.net/projects/extrema|{{AUR|extrema}}}} | + | * {{App|Extrema|Visualization and data analysis tool.|http://sourceforge.net/projects/extrema|{{AUR|extrema}}{{Broken package link|{{aur-mirror|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.|http://labplot.sourceforge.net/|{{AUR|labplot2}}{{Broken package link|{{aur-mirror|labplot2}}}}}} |
− | * {{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:// | + | * {{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 | + | See also [[List of applications#Spreadsheets]] |
=== Chemistry and biology === | === Chemistry and biology === | ||
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====Computational biology and bioinformatics==== | ====Computational biology and bioinformatics==== | ||
− | + | 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 | + | * {{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 | + | * {{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|{{ | + | * {{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/ | + | * {{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}}}} | ||
− | ==== | + | ==== Molecules ==== |
− | + | ===== 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|{{ | + | * {{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}}}}}} |
− | ==== | + | ===== 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}}}} | ||
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* {{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}}}} | + | * {{App|[[Wikipedia:XDrawChem|XDrawChem]]|Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).|http://xdrawchem.sourceforge.net/|{{AUR|xdrawchem}}{{Broken package link|{{aur-mirror|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}}{{Broken package link|{{aur-mirror|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}}}} | ||
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==== Biochemistry ==== | ==== Biochemistry ==== | ||
− | * {{App|[[Wikipedia:Bioclipse|Bioclipse]]|Java-based visual platform for | + | * {{App|[[Wikipedia:Bioclipse|Bioclipse]]|Java-based visual platform for biochemistry that uses the Eclipse Rich Client Platform (RCP).|http://www.bioclipse.net/|{{AUR?|bioclipse}}}} |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
==== 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 132: | Line 147: | ||
* {{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| | + | * {{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://code.google.com/p/open-phd-guiding/|{{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 144: | Line 160: | ||
==== Electronics ==== | ==== 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. | ||
+ | |||
+ | * {{App|atanua|Real time logic simulator.|http://sol.gfxile.net/atanua/|{{AUR|atanua}}{{Broken package link|{{aur-mirror|atanua}}}}}} | ||
+ | * {{App|eqntott|Utility to convert a set of boolean logic equations to a PLA-esque truth table.|https://code.google.com/p/eqntott/|{{AUR|eqntott}}{{Broken package link|{{aur-mirror|eqntott}}}}}} | ||
+ | * {{App|espresso|Heuristic logic minimizer, reduces the amount of gates required for digital circuits.|https://code.google.com/p/eqntott/|{{AUR|espresso}}{{Broken package link|{{aur-mirror|espresso}}}}}} | ||
+ | * {{App|giraffe|A simple logic circuit simulator written in Java.|http://nbenoit.tuxfamily.org/|{{AUR|giraffe}}{{Broken package link|{{aur-mirror|giraffe}}}}}} | ||
+ | * {{App|glogic|An educational graphical logic circuit simulator.|https://launchpad.net/glogic|{{AUR|glogic}}}} | ||
+ | * {{App|KLogic|Digital logic design and simulation software for KDE which also simulate karnaugh diagrams.|http://www.a-rostin.de/|{{AUR|klogic}}{{Broken package link|{{aur-mirror|klogic}}}}}} | ||
+ | * {{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}}{{Broken package link|{{aur-mirror|logisim-evolution}}}}}} | ||
+ | * {{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}}}} | ||
+ | * {{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/|{{AUR|ktechlab-zoltan_p-git}}{{Broken package link|{{aur-mirror|ktechlab-zoltan_p-git}}}}}} | ||
+ | |||
+ | ===== 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|[[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: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/ | + | |
* {{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 156: | Line 196: | ||
==== 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| | + | * {{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 164: | Line 206: | ||
* {{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 06:26, 22 August 2016
Contents
Science
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.
- calc — Arbitrary precision console calculator.
- Extcalc — Qt-based scientfic graphical calculator.
- galculator — GTK+ based scientific calculator.
- GNOME Calculator — Scientific calculator included in the GNOME desktop.
- GCalctool — Scientific calculator included in the GNOME desktop (old GTK2 version).
- 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.
- 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}
- 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}^{[broken link: archived in aur-mirror]}
- GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.
- Maple — Famous commercial CAS. Often used in education.
- http://www.maplesoft.com/products/maple/ || not packaged? search in AUR
- 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 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
See also Wikipedia:Comparison of numerical analysis software.
- 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}^{[broken link: archived in aur-mirror]}
- 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.
- GNU Radio — Software development toolkit that provides signal processing blocks to implement software radios.
- matplotlib (PyLab) — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
- Sage-mathematics — 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
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}
- 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.
- 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}
- RStudio — A powerful and productive IDE for R written in Qt.
Data evaluation
See also Wikipedia:List of information graphics software.
- Extrema — Visualization and data analysis tool.
- http://sourceforge.net/projects/extrema || extrema^{AUR}^{[broken link: archived in aur-mirror]}
- 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}^{[broken link: archived in aur-mirror]}
- 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
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}
- 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}
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).
- 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.
- 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}^{[broken link: archived in aur-mirror]}
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).
- http://xdrawchem.sourceforge.net/ || xdrawchem^{AUR}^{[broken link: archived in aur-mirror]}
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).
- http://www.quantum-espresso.org/ || quantum-espresso^{AUR}^{[broken link: archived in aur-mirror]}
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 from the KDE desktop.
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 || 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.
- http://code.google.com/p/open-phd-guiding/ || open-phd-guiding-svn^{AUR}^{[broken link: archived in aur-mirror]}
- 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.
- Where Is M13 — Application to visualize the locations and physical properties of deep sky objects.
- XEphem — Motif-based ephemeris and planetarium program.
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.
- atanua — Real time logic simulator.
- http://sol.gfxile.net/atanua/ || atanua^{AUR}^{[broken link: archived in aur-mirror]}
- eqntott — Utility to convert a set of boolean logic equations to a PLA-esque truth table.
- https://code.google.com/p/eqntott/ || eqntott^{AUR}^{[broken link: archived in aur-mirror]}
- espresso — Heuristic logic minimizer, reduces the amount of gates required for digital circuits.
- https://code.google.com/p/eqntott/ || espresso^{AUR}^{[broken link: archived in aur-mirror]}
- giraffe — A simple logic circuit simulator written in Java.
- http://nbenoit.tuxfamily.org/ || giraffe^{AUR}^{[broken link: archived in aur-mirror]}
- glogic — An educational graphical logic circuit simulator.
- https://launchpad.net/glogic || glogic^{AUR}
- KLogic — Digital logic design and simulation software for KDE which also simulate karnaugh diagrams.
- http://www.a-rostin.de/ || klogic^{AUR}^{[broken link: archived in aur-mirror]}
- 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.
- https://github.com/reds-heig/logisim-evolution || logisim-evolution^{AUR}^{[broken link: archived in aur-mirror]}
- 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-git^{AUR}
HDL
- 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.
- 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/ || ktechlab-zoltan_p-git^{AUR}^{[broken link: archived in aur-mirror]}
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.
- 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.
- 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.
- EPANET — EPANET performs extended period simulation of the water movement and quality behavior within pressurized pipe networks.
- http://www.epa.gov/ || epanet2-git^{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.
Geography
- GNOME Maps — A simple map client for GNOME. Part of gnome-extra.
- JOSM — An editor for OpenStreetMap written in Java.
- Marble — Virtual Globe and World Atlas that can be used to learn more about the Earth. Part of kdeedu.
- Merkaartor — OpenStreetMap editor.
- Viking — GTK+2 application to manage GPS data.