List of applications/Science
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Revision as of 20:11, 19 May 2013 by Karol (Talk | contribs) (→Computational Biology and Bioinformatics: posted links for biopython in the AUR)
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Contents
Science
Scientific Documents
Mathematics
Calculator
- bc — An arbitrary precision calculator language.
- calc — An arbitrary precision console calculator.
- Extcalc — A Qt-based scientfic graphical calculator.
- GCalctool — A scientific calculator included in the GNOME desktop.
- http://www.gnome.org || gcalctool-oldgui^{AUR}
- KAlgebra — A calculator and 3D plotter included in KDE EDU.
- KCalc — A scientific calculator included in the KDE desktop.
- Qalculate — A calculator and equation solver with fault-tolerant parsing, constant recognition and units.
- SpeedCrunch — A fast, high precision and powerful cross-platform calculator.
- http://speedcrunch.org || speedcrunch^{AUR}
- xcalc — A scientific calculator for X with algebraic and reverse polish notation modes.
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/ || fermat^{AUR}
- Mathomatic — A general purpose Computer Algebra System written in C.
- Maxima — A Maple/Mathematica-like program with a wxWidgets based frontend.
- PARI/GP — A computer algebra system designed for fast computations in number theory.
- Sage — A algebra system similar to Maxima, but written in Python.
- Xcas — A user interface to Giac, a free, basic computer algebra system.
Scientific or Technical Computing
- EngLab — A cross-compile mathematical platform with a C like syntax.
- http://englab.bugfest.net || englab^{AUR}
- 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 || euler^{AUR}
- 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.
- PyLab — A collection of Python modules (pyplot, numpy, etc.) used for scientific calculations.
- 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/ || scilab^{AUR}
Statistics
- 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/ || jags^{AUR}
- PSPP — A free SPSS implementation.
- http://www.gnu.org/software/pspp/ || pspp^{AUR}
- R — A software environment for statistical computing and graphics.
- RKWard — A frontend for the statistical language R.
Data Evaluation
- Extrema — A visualization and data analysis tool.
- Fityk — A curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.
- http://fityk.nieto.pl/ || fityk^{AUR}
- Gnuplot — A command-line program that can generate 2D and 3D plots of functions, data, and data fits.
- Grace — A WYSIWYG 2D graph plotting tool.
- http://plasma-gate.weizmann.ac.il/Grace/ || grace qtgrace^{AUR} gracegtk^{AUR}
- LabPlot — A free software data analysis and visualization application, similar to SciDAVis.
- http://labplot.sourceforge.net/ || labplot2^{AUR}
- QtiPlot — A platform-independent application used for interactive scientific graphing and data analysis, similar to the proprietary Origin or SigmaPlot.
- ROOT — A data analysis program and library (originally for particle physics) developed by CERN.
- http://root.cern.ch/drupal/ || root^{AUR}
- SciDAVis — A fork of QtiPlot with the goal of being better documented and more user friendly.
- http://scidavis.sourceforge.net/ || scidavis^{AUR}
See also List of Applications#Spreadsheets
Chemistry and Biology
Computational Biology and Bioinformatics
- BALL (Biochemical Algorithms Library) — 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/ || ball^{AUR}
- BioJava — A set of Java tools for computational biology, as well as bioinformatics.
- http://biojava.org/wiki/Main_Page || biojava^{AUR}
- Biopython — A Python package with tools for computational biology, as well as bioinformatics.
- http://biopython.org/wiki/Biopython || python-biopython^{AUR} python2-biopython^{AUR}
- EMBOSS (European Molecular Biology Open Software Suite) — An 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) — 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/ || mega^{AUR}
- MUMmer — A bioinformatics software system for sequence alignment based on suffix trees.
- http://mummer.sourceforge.net/ || mummer^{AUR}
- 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/ || ugene^{AUR}
Molecule Viewer
- Avogadro — An editor, viewer and simulator for 3D molecule structures (also supports downloading files from the Protein Data Bank).
- BALLView — A standalone molecular modeling and visualization application, part of the BALL framework.
- http://www.ballview.org/ || ball^{AUR}
- Ghemical — A computational chemistry software package used to edit, view and simulate molecular structures.
- 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.sourceforge.net/ || pymol^{AUR}
- 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/ || rasmol^{AUR}
Molecule Drawing
- BKChem — A practical and goodlooking skeletal formula molecule drawing program.
- http://bkchem.zirael.org/ || bkchem^{AUR}
- Chemtool — A GTK+-based program for drawing chemical structural formulas.
- EasyChem — A simple skeletal formula molecule drawing program with a focus on producing press-quality figures.
- http://easychem.sourceforge.net/ || easychem^{AUR}
- Gabedit — A 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 — An extensive skeletal formula molecule drawing program (includes spectroscopy prediction).
Periodic Table
- gElemental — A periodic table of the elements with additional information.
- Kalzium — A periodic table of the elements with molecule editor and equation solver from the KDE desktop.
Biochemistry
- Bioclipse — A 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) — 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 || gromacs^{AUR}
- 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).
Image manipulation
- 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 || imagej^{AUR}
Astronomy
- 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.
- GIMP Astronomy Plugins — A set of GIMP plugins for astronomical image processing.
- GoQat — A 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 — 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.
- Open PHD Guiding — A telescope autoguiding software based on the famous PHD Guiding.
- Qastrocam-g2 — A webcam acquisition software for planetary imaging.
- 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.
- StarPlot — A 3-dimensional star chart viewer.
- http://starplot.org/ || starplot^{AUR}
- Stellarium — A beautiful 3D planetarium that uses OpenGL to render a realistic sky in real time.
- XEphem — A Motif-based ephemeris and planetarium program.
Physics
Electronics
- gEDA — A full suite and toolkit of Electronic Design Automation tools that are used for electrical circuit design, schematic capture, simulation, prototyping, and production.
- 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).
- KLogic — An application used for easily building and simulating digital circuits.
- http://www.a-rostin.de/ || klogic^{AUR}
- 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.
- Oregano — A graphical software application for schematic capture and simulation of electrical circuits. The actual simulation is done by the ngspice or Gnucap engines.
- QElectroTech — An application used to draw advanced electrical circuits.
- http://qelectrotech.org/ || qelectrotech^{AUR}
- 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.
Physics Simulation
- Code_Aster — A software package for Civil and Structural Engineering finite element analysis and numeric simulation in structural mechanics.
- http://www.code-aster.org || aster^{AUR}
- Step — A two-dimensional physics simulation engine that is included in the KDE desktop as part of KDE Edu.
Unit Conversion
- 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/ || convertall^{AUR}
- Gonvert — A conversion utility that allows conversion between many units like CGS, Ancient, Imperial with many categories like length, mass, numbers, etc.
- 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.