Difference between revisions of "List of applications/Science"

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[[Category:Mathematics and science]]
 
[[Category:Mathematics and science]]
 
[[Category:Applications]]
 
[[Category:Applications]]
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[[es:List of Applications/Science]]
 
[[it:List of Applications/Science]]
 
[[it:List of Applications/Science]]
 
[[ja:List of Applications/Science]]
 
[[ja:List of Applications/Science]]
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{{List of Applications navigation}}
 
{{List of Applications navigation}}
 
</noinclude>
 
</noinclude>
 +
 
== Science ==
 
== Science ==
 +
 
{{Note|1=For possibly more up to date selection of scientific applications, try checking the [https://aur.archlinux.org/packages.php?O=0&do_Search=Go&detail=1&C=15&SeB=nd&SB=v&SO=d&PP=50 AUR 'science' category]}}
 
{{Note|1=For possibly more up to date selection of scientific applications, try checking the [https://aur.archlinux.org/packages.php?O=0&do_Search=Go&detail=1&C=15&SeB=nd&SB=v&SO=d&PP=50 AUR 'science' category]}}
  
=== Scientific Documents ===
+
=== Scientific documents ===
 +
 
 
{{Box||See the main article: [[List of Applications/Documents#Scientific Documents]]|#E5E5FF|#FCFCFC}}
 
{{Box||See the main article: [[List of Applications/Documents#Scientific Documents]]|#E5E5FF|#FCFCFC}}
  
 
=== Mathematics ===
 
=== Mathematics ===
 +
 
==== Calculator ====
 
==== Calculator ====
 +
 
{{Wikipedia|Comparison of software calculators}}
 
{{Wikipedia|Comparison of software calculators}}
  
* {{App|[[Wikipedia:bc programming language|bc]]|An 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|An 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|A 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]]|A scientific calculator included in the GNOME desktop.|http://www.gnome.org|{{AUR|gcalctool-oldgui}}}}
+
* {{App|[[Wikipedia:GCalctool|GCalctool]]|Scientific calculator included in the GNOME desktop.|http://www.gnome.org|{{AUR|gcalctool-oldgui}}}}
* {{App|KAlgebra|A calculator and 3D plotter included in KDE EDU.|http://www.kde.org/applications/education/kalgebra/|{{Pkg|kdeedu-kalgebra}}}}
+
* {{App|KAlgebra|Calculator and 3D plotter included in KDE EDU.|http://www.kde.org/applications/education/kalgebra/|{{Pkg|kdeedu-kalgebra}}}}
* {{App|[[Wikipedia:KCalc|KCalc]]|A scientific calculator included in the KDE desktop.|http://kde.org/applications/utilities/kcalc/|{{Pkg|kdeutils-kcalc}}}}
+
* {{App|[[Wikipedia:KCalc|KCalc]]|Scientific calculator included in the KDE desktop.|http://kde.org/applications/utilities/kcalc/|{{Pkg|kdeutils-kcalc}}}}
* {{App|Qalculate|A calculator and equation solver with fault-tolerant parsing, constant recognition and units.|http://qalculate.sourceforge.net/|{{Pkg|libqalculate}}}}
+
* {{App|Qalculate|Calculator and equation solver with fault-tolerant parsing, constant recognition and units.|http://qalculate.sourceforge.net/|{{Pkg|libqalculate}}}}
* {{App|SpeedCrunch|A fast, high precision and powerful cross-platform calculator.|http://speedcrunch.org|{{AUR|speedcrunch}}}}
+
* {{App|SpeedCrunch|Fast, high precision and powerful cross-platform calculator.|http://speedcrunch.org|{{AUR|speedcrunch}}}}
* {{App|[[Wikipedia:xcalc|xcalc]]|A 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}}
 
{{Wikipedia|Comparison of computer algebra systems}}
  
* {{App|[[Wikipedia:Fermat (computer algebra system)|Fermat]]|A computer algebra system that does arithmetic of arbitrarily long integers and fractions, multivariate polynomials, symbolic calculations, matrices over polynomial rings, graphics, and other numerical calculations.|http://home.bway.net/lewis/|{{AUR|fermat}}}}
+
* {{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:Mathomatic|Mathomatic]]|A general purpose Computer Algebra System written in C.|http://www.mathomatic.org/|{{Pkg|mathomatic}}}}
+
* {{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:Maxima (software)|Maxima]]|A [[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:Mathomatic|Mathomatic]]|General purpose Computer Algebra System written in C.|http://www.mathomatic.org/|{{Pkg|mathomatic}}}}
* {{App|[[Wikipedia:PARI/GP|PARI/GP]]|A computer algebra system designed for fast computations in number theory.|http://pari.math.u-bordeaux.fr/|{{Pkg|pari}}}}
+
* {{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|[[Sage]]|A algebra system similar to Maxima, but written in Python.|http://www.sagemath.org/|{{Pkg|sage-mathematics}}}}
+
* {{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]]|A 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 ====
 
 
{{Wikipedia|Comparison of numerical analysis software}}
 
{{Wikipedia|Comparison of numerical analysis software}}
  
* {{App|EngLab|A 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]]|A 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}}}}
* {{App|[[Wikipedia:FreeMat|FreeMat]]|A Matlab-like program that supports many of its functions and features a codeless interface to external C, C++, and Fortran code, further parallel distributed algorithm development (via MPI), and 3D visualization capabilities.|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|[[Octave]]|A [[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]]|A collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.|http://www.scipy.org/PyLab|{{Pkg|python2-matplotlib}}}}
+
* {{App|[[Wikipedia:matplotlib|PyLab]]|Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.|http://www.scipy.org/PyLab|{{Pkg|python2-matplotlib}}}}
* {{App|[[Wikipedia:Scilab|Scilab]]|A Matlab alternative used for numerical computations, its syntax is not equivalent to that of Matlab, but it can be easily converted.|http://www.scilab.org/|{{AUR|scilab}}}}
+
* {{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}}}}
  
 
==== Statistics ====
 
==== Statistics ====
 +
 
{{Wikipedia|Comparison of statistical packages}}
 
{{Wikipedia|Comparison of statistical packages}}
  
* {{App|[[Wikipedia:Just another Gibbs sampler|JAGS]] (Just another Gibbs sampler)|A cross-platform program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.|http://mcmc-jags.sourceforge.net/|{{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:PSPP|PSPP]]|A 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]]|A 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]]|A frontend for the statistical language R.|http://rkward.sourceforge.net/{{linkrot|2013|05|19}}|{{AUR|rkward}}}}
+
* {{App|[[Wikipedia:RKWard|RKWard]]|Frontend for the statistical language R.|http://rkward.sourceforge.net/|{{AUR|rkward}}}}
 +
 
 +
==== Data evaluation ====
  
==== Data Evaluation ====
 
 
{{Wikipedia|List of information graphics software}}
 
{{Wikipedia|List of information graphics software}}
  
* {{App|Extrema|A 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}}}}
* {{App|[[Wikipedia:Fityk|Fityk]]|A 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]]|A 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]]|A 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]]|A 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}}}}
* {{App|[[Wikipedia:QtiPlot|QtiPlot]]|A 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://soft.proindependent.com/qtiplot.html|{{Pkg|qtiplot}}}}
* {{App|[[Wikipedia:ROOT|ROOT]]|A 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]]|A 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 ===
====Computational Biology and Bioinformatics====
+
 
 +
====Computational biology and bioinformatics====
 +
 
 
{{Wikipedia|List of open source bioinformatics software}}
 
{{Wikipedia|List of open source bioinformatics software}}
  
* {{App|[[Wikipedia:BALL|BALL]] (Biochemical Algorithms Library)|An application framework in C++ that provides an extensive set of data structures as well as classes for molecular nechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.|http://www.ball-project.org/|{{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 nechanics, 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]]|A 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/wiki/Main_Page|{{AUR|biojava}}}}
* {{App|[[Wikipedia:Biopython|Biopython]]|A 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|{{AUR|python-biopython}} {{AUR|python2-biopython}}}}
* {{App|[[Wikipedia:EMBOSS|EMBOSS]] (European Molecular Biology Open Software Suite)|An open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community.|http://emboss.sourceforge.net/|{{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)|An integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses.|http://www.megasoftware.net/|{{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/|{{AUR|mega}}}}
* {{App|[[Wikipedia:MUMmer|MUMmer]]|A 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]]|An 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 ====
  
==== Molecule Viewer ====
 
 
{{Wikipedia|List of molecular graphics systems}}
 
{{Wikipedia|List of molecular graphics systems}}
  
* {{App|[[Wikipedia:Avogadro_(software)|Avogadro]]|An 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|A 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]]|A 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]]|An 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|{{AUR|pymol}}}}
* {{App|[[Wikipedia:RasMol|RasMol]]|A computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures.|http://www.rasmol.org/|{{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}}}}
 +
 
 +
==== Molecule drawing ====
 +
 
 +
* {{App|[[Wikipedia:BKchem|BKChem]]|Practical and goodlooking skeletal formula molecule drawing program.|http://bkchem.zirael.org/|{{AUR|bkchem}}}}
 +
* {{App|[[Wikipedia:Chemtool|Chemtool]]|GTK+-based program for drawing chemical structural formulas.|http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html|{{Pkg|chemtool}}}}
 +
* {{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:XDrawChem|XDrawChem]]|Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).|http://xdrawchem.sourceforge.net/|{{AUR|xdrawchem}}}}
  
==== Molecule Drawing ====
+
==== Periodic table ====
* {{App|[[Wikipedia:BKchem|BKChem]]|A practical and goodlooking skeletal formula molecule drawing program.|http://bkchem.zirael.org/|{{AUR|bkchem}}}}
+
* {{App|[[Wikipedia:Chemtool|Chemtool]]|A GTK+-based program for drawing chemical structural formulas.|http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html|{{Pkg|chemtool}}}}
+
* {{App|EasyChem|A simple skeletal formula molecule drawing program with a focus on producing press-quality figures.|http://easychem.sourceforge.net/|{{AUR?|easychem}}}}
+
* {{App|[[Wikipedia:Gabedit|Gabedit]]|A 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]]|An extensive skeletal formula molecule drawing program (includes spectroscopy prediction).|http://xdrawchem.sourceforge.net/|{{AUR|xdrawchem}}}}
+
  
==== Periodic Table ====
+
* {{App|gElemental|Periodic table of the elements with additional information.|http://freshmeat.net/projects/gelemental|{{AUR|gelemental}}}}
* {{App|gElemental|A 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]]|A periodic table of the elements with molecule editor and equation solver from the [[KDE]] desktop.|http://edu.kde.org/kalzium/|{{Pkg|kdeedu-kalzium}}}}
+
  
 
==== Biochemistry ====
 
==== Biochemistry ====
* {{App|[[Wikipedia:Bioclipse|Bioclipse]]|A Java-based visual platform for biochemestry that uses the Eclipse Rich Client Platform (RCP).|http://www.bioclipse.net/|{{AUR?|bioclipse}}}}
 
  
==== Molecular Modeling ====
+
* {{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:GROMACS|GROMACS]] (GROningen MAchine for Chemical Simulations)|A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.|http://www.gromacs.org|{{AUR|gromacs}}}}  
+
 
* {{App|[[Wikipedia:Quantum ESPRESSO|Quantum ESPRESSO]]|An integrated suite of applications for electronic-structure calculations and materials modeling at nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).|http://www.quantum-espresso.org/|{{AUR|quantum-espresso}}}}
+
==== 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]]|A Java-based image processing and analysing program that provides extensibility via plugins and macros. It is widely used in microscopy (e.g. for cell counting).|http://rsb.info.nih.gov/ij|{{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 ===
  
* {{App|[[Wikipedia:Celestia|Celestia]]|A 3D astronomy simulation program that allows users to travel through an extensive universe, modeled after reality, at any speed, in any direction and at any time in history.|http://www.shatters.net/celestia/|{{Pkg|celestia}}}}
+
* {{App|[[Wikipedia:Celestia|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/|{{Pkg|celestia}}}}
* {{App|GIMP Astronomy Plugins|A 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|A 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]]|A planetarium application that provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. It is included in KDE Edu.|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|kdeedu-kstars}}}}
* {{App|Open PHD Guiding|A 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}}}}
* {{App|Qastrocam-g2|A 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]]|A planetarium that maps out and labels most of the constellations, planets, and objects you can see with a telescope. It can also download Digitized Sky Survey Charts and superimpose images over these charts.|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|A 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]]|A 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|[[Wikipedia:XEphem|XEphem]]|A 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}}}}
  
 
=== Physics ===
 
=== Physics ===
 +
 
==== Electronics ====
 
==== Electronics ====
 +
 
{{Wikipedia|Comparison of EDA software}}
 
{{Wikipedia|Comparison of EDA software}}
  
* {{App|[[gEDA]]|A 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]]|A software suite for electronic design automation (EDA) that facilitates the design of schematics for electronic circuits and their conversion to PCB (printed circuit board).|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|An application used for easily building and simulating digital circuits.|http://www.a-rostin.de/|{{AUR|klogic}}}}
+
* {{App|KLogic|Application used for easily building and simulating digital circuits.|http://www.a-rostin.de/|{{AUR|klogic}}}}
* {{App|[[Wikipedia:KTechLab|KTechLab]]|An IDE for electronic and PIC microcontroller circuit design and simulation featuring an extensive circuit designer with autorouting and simulation of all common electronic components and logic elements.|http://sourceforge.net/projects/ktechlab/|{{Pkg|ktechlab}}}}
+
* {{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]]|A 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|[[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|An 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]]|An electronics circuit simulator application that gives you the ability to set up a circuit with a graphical user interface and simulate its large-signal, small-signal and noise behaviour.|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}}}}
 +
 
 +
==== 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: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}}}}
  
==== Physics Simulation ====
+
==== Unit conversion ====
* {{App|[[Wikipedia:Code_Aster|Code_Aster]]|A 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:Step (software)|Step]]|A 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}}}}
+
  
==== Unit Conversion ====
+
* {{App|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/|{{AUR|convertall}}}}  
* {{App|ConvertAll|A unit conversion application that allows one to combine units in any way (e.g. inches per decade), even if it does not make sense.|http://convertall.bellz.org/|{{AUR|convertall}}}}  
+
* {{App|Gonvert|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|A conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.|http://www.unihedron.com/projects/gonvert/|{{AUR|gonvert}}}}  
+
* {{App|[[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]]|A command-line unit converter and calculator that can handle multiplicative scale changes, nonlinear conversions such as Fahrenheit to Celsius or wire gauge and others.|http://www.gnu.org/s/units/|{{Pkg|units}}}}
+

Revision as of 15:13, 15 October 2013

Template:List of Applications navigation


Science

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

Scientific documents

Template:Box

Mathematics

Calculator

Template:Wikipedia

  • 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
  • GCalctool — Scientific calculator included in the GNOME desktop.
http://www.gnome.org || gcalctool-oldguiAUR
  • KAlgebra — Calculator and 3D plotter included in KDE EDU.
http://www.kde.org/applications/education/kalgebra/ || kdeedu-kalgebra
  • KCalc — Scientific calculator included in the KDE desktop.
http://kde.org/applications/utilities/kcalc/ || kdeutils-kcalc
  • Qalculate — Calculator and equation solver with fault-tolerant parsing, constant recognition and units.
http://qalculate.sourceforge.net/ || libqalculate
  • SpeedCrunch — Fast, high precision and powerful cross-platform calculator.
http://speedcrunch.org || speedcrunchAUR
  • xcalc — Scientific calculator for X with algebraic and reverse polish notation modes.
http://xorg.freedesktop.org/ || xorg-xcalc

Computer algebra system

Template:Wikipedia

  • 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
  • GAP — Computer algebra system for computational discrete algebra with particular emphasis on computational group theory.
http://www.gap-system.org || gap-mathAUR
  • 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 || xcasAUR

Scientific or technical computing

Template:Wikipedia

  • EngLab — Cross-compile mathematical platform with a C like syntax.
http://englab.bugfest.net || englabAUR
  • Euler — Numerical application designed for higher level math such as calculus, optimization, and statistics that uses Maxima for symbolic operations.
http://euler.sourceforge.net || eulerAUR
  • 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
  • OctaveMatlab-like language and interface for numerical computations.
http://www.gnu.org/software/octave/ || octave
  • PyLab — Collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
http://www.scipy.org/PyLab || python2-matplotlib
  • 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 || sage-mathematics
  • 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

Template:Wikipedia

  • 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
  • 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

Data evaluation

Template:Wikipedia

  • Extrema — Visualization and data analysis tool.
http://sourceforge.net/projects/extrema || extremaAUR
  • 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.
http://labplot.sourceforge.net/ || labplot2AUR
  • QtiPlot — Platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.
http://soft.proindependent.com/qtiplot.html || 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

Template:Wikipedia

  • 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/ || ballAUR
  • BioJava — Set of Java tools for computational biology, as well as bioinformatics.
http://biojava.org/wiki/Main_Page || biojavaAUR
  • Biopython — Python package with tools for computational biology, as well as bioinformatics.
http://biopython.org/wiki/Biopython || python-biopythonAUR python2-biopythonAUR
  • 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/ || megaAUR
  • 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

Molecule viewer

Template:Wikipedia

  • 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 || pymolAUR
  • 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

Molecule 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
  • XDrawChem — Extensive skeletal formula molecule drawing program (includes spectroscopy prediction).
http://xdrawchem.sourceforge.net/ || xdrawchemAUR

Periodic table

  • 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 biochemestry that uses the Eclipse Rich Client Platform (RCP).
http://www.bioclipse.net/ || not packaged? search in AUR

Molecular modeling

  • GROMACS (GROningen MAchine for Chemical Simulations) — Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
http://www.gromacs.org || 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

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/ || kdeedu-kstars
  • Open PHD Guiding — Telescope autoguiding software based on the famous PHD Guiding.
http://code.google.com/p/open-phd-guiding/ || open-phd-guiding-svnAUR
  • 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
  • XEphem — Motif-based ephemeris and planetarium program.
http://www.clearskyinstitute.com/xephem/xephem.html || xephemAUR

Physics

Electronics

Template:Wikipedia

  • 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
  • KLogic — Application used for easily building and simulating digital circuits.
http://www.a-rostin.de/ || klogicAUR
  • 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
  • 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/marc-lorber/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 || asterAUR
  • Step — Two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.
http://edu.kde.org/step/ || kdeedu-step

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