Software tools: Difference between revisions

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On this page, a list of useful publicly available software tools, for data analysis, graphical display, etc. should be provided.
On this page, you will find a list of useful publicly available software tools, for data analysis, graphical display, etc.


== Emulation ==
== Emulation, file management ==


* [http://xquartz.macosforge.org/landing/ XQuartz] X-window system for Mac
* [http://xquartz.macosforge.org/landing/ XQuartz] X-window system for Mac
* [http://mobaxterm.mobatek.net/ MobaXterm] X-window system for Windows
* [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] Telnet/SSH client for Windows and Unix
* [http://www.chiark.greenend.org.uk/~sgtatham/putty/ PuTTY] Telnet/SSH client for Windows and Unix
* [http://rsug.itd.umich.edu/software/fugu/ Fugu] Secure File Transfer for Mac


== Numerical tools and libraries ==
== Numerical tools and libraries ==
* [https://www.nr.com/ Numerical Recipes]
* [https://gcc.gnu.org/wiki/GFortran GNU Fortran]
* [https://www.gnu.org/software/octave/ Octave], a free alternative to [http://www.mathworks.com/products/matlab/ Matlab]
* [https://www.python.org/ Python], a programming language
** [https://www.enthought.com/products/canopy/ Canopy] Scientific and Analytic Python Deployment with Integrated Analysis Environment
** [https://docs.anaconda.com/anaconda/ Anaconda] Python distribution for large-scale data processing, predictive analytics, and scientific computing
** [https://www.sagemath.org/ SageMath] Free open-source mathematics software system licensed under the GPL. Its mission is to create a viable free open source alternative to Magma, Maple, Mathematica and Matlab
** [https://jupyter.org/ Jupyter] and [http://ipython.org/ IPython] Powerful browser-based notebook and interactive shells for Python and other languages
** [https://www.numpy.org/ NumPy] and [https://www.scipy.org/ Scipy] Fundamental packages for scientific computing with Python
** [https://matplotlib.org/ matplotlib] A python plotting library that produces publication quality figures
** [https://seaborn.pydata.org/ Seaborn] Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics
** [https://pythonhosted.org/spyder/ Spyder] Open source cross-platform Integrated Development Environment for scientific programming in the Python language. Spyder integrates NumPy, SciPy, Matplotlib and IPython, as well as other open source software
** [https://www.jetbrains.com/pycharm/ PyCharm] PyCharm is an Integrated Development Environment used for programming in Python. It provides code analysis, a graphical debugger, an integrated unit tester, integration with version control systems, and supports web development with Django
** [http://vpython.org/ VPython] Python programming language plus a 3D graphics module called "visual". VPython makes it easy to create navigable 3D displays and animations
** [http://docs.enthought.com/mayavi/mayavi/ Mayavi] An application and library for interactive scientific data visualization and 3D plotting in Python
** [https://yt-project.org/ yt] An open-source python package for analyzing and visualizing volumetric data
** [https://pandas.pydata.org/ pandas] and [http://xarray.pydata.org/en/stable/ xarray] Easy-to-use data structures and data analysis tools for Python
** [http://www.pytables.org/ pytables] and [http://www.h5py.org/ h5py] Tools for using HDF5 data in Python
** [http://cython.org/ Cython] and [https://numba.pydata.org/ Numba] Tools that allow compiled speeds in Python
** [https://gafusion.github.io/OMFIT-source/ OMFIT] Software that supports integrated modeling and experimental data analysis of magnetically confined thermonuclear fusion experiments.
** [https://github.com/PlasmaPy/PlasmaPy/ PlasmaPy] An open source core Python package for plasma physics that is under development


== Mathematical tools ==
== Mathematical tools ==
* [https://mathics.angusgriffith.com/ Mathics], a free alternative to [http://www.wolfram.com/mathematica/ Mathematica]
* [http://live.sympy.org/ SymPy], symbolic calculus using Python
* [http://people.math.sfu.ca/~cbm/aands/ Abramowitz and Stegun: Handbook of Mathematical Functions]


== Graphical tools ==
== Graphical tools ==


* [http://www.gnuplot.info/ GNUplot], also see [http://www.gnuplotting.org/ gnuplotting.org]
* [http://www.gnuplot.info/ GNUplot], also see [http://www.gnuplotting.org/ gnuplotting.org], for producing graphs from data
* [http://www.gimp.org/ GIMP], graphics editor
* [http://rsb.info.nih.gov/ij/features.html ImageJ], graphics editor and image analysis
* [https://inkscape.org/ InkScape], [[:Wikipedia:vector graphics|vector graphics]] editor
* [https://wci.llnl.gov/simulation/computer-codes/visit/ VisIt], an open Source, interactive, scalable, visualization, animation and analysis tool


== Text editing tools ==
== Text editing tools ==


* [http://en.wikibooks.org/wiki/LaTeX LaTeX]
* [http://en.wikibooks.org/wiki/LaTeX LaTeX]
** [http://pages.uoregon.edu/koch/texshop/ TeXShop] (Complete LaTeX + BibTeX package, for Mac)
** [http://pages.uoregon.edu/koch/texshop/ TeXShop], complete LaTeX + BibTeX package for Mac
** [http://bibdesk.sourceforge.net/ BibDesk] (Bibliography manager, for Mac)
** [http://bibdesk.sourceforge.net/ BibDesk], bibliography manager for Mac
** [http://www.chachatelier.fr/latexit/ LaTeXiT] (Compile LaTeX formula for presentations, for Mac)
** [http://www.chachatelier.fr/latexit/ LaTeXiT], compiles LaTeX formulas for presentations for Mac
* [http://www.gnu.org/software/emacs/ Emacs]
** [https://www.sharelatex.com ShareLaTeX] and [https://www.overleaf.com/ Overleaf], collaborative writing websites for LaTeX
** [https://3142.nl/latex-diff/ LatexDiff], to compare different versions of a document and highlight changes
* [http://www.gnu.org/software/emacs/ Emacs], powerful plain text editor
* [http://www.barebones.com/products/textwrangler/ TextWrangler], powerful plain text editor for Mac
* [https://www.libreoffice.org/ LibreOffice], office suite of programs
* [https://www.authorea.com/ Authorea], a power collaborative writing website


== See also ==
== See also ==


* [http://connectedresearchers.com/online-tools-for-researchers/ Digital tools for researchers]
* [http://connectedresearchers.com/online-tools-for-researchers/ Digital tools for researchers]
* [[:Wikipedia:List of revision control software|List of revision control software]]

Latest revision as of 20:34, 18 November 2018

On this page, you will find a list of useful publicly available software tools, for data analysis, graphical display, etc.

Emulation, file management

  • XQuartz X-window system for Mac
  • MobaXterm X-window system for Windows
  • PuTTY Telnet/SSH client for Windows and Unix
  • Fugu Secure File Transfer for Mac

Numerical tools and libraries

  • Numerical Recipes
  • GNU Fortran
  • Octave, a free alternative to Matlab
  • Python, a programming language
    • Canopy Scientific and Analytic Python Deployment with Integrated Analysis Environment
    • Anaconda Python distribution for large-scale data processing, predictive analytics, and scientific computing
    • SageMath Free open-source mathematics software system licensed under the GPL. Its mission is to create a viable free open source alternative to Magma, Maple, Mathematica and Matlab
    • Jupyter and IPython Powerful browser-based notebook and interactive shells for Python and other languages
    • NumPy and Scipy Fundamental packages for scientific computing with Python
    • matplotlib A python plotting library that produces publication quality figures
    • Seaborn Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics
    • Spyder Open source cross-platform Integrated Development Environment for scientific programming in the Python language. Spyder integrates NumPy, SciPy, Matplotlib and IPython, as well as other open source software
    • PyCharm PyCharm is an Integrated Development Environment used for programming in Python. It provides code analysis, a graphical debugger, an integrated unit tester, integration with version control systems, and supports web development with Django
    • VPython Python programming language plus a 3D graphics module called "visual". VPython makes it easy to create navigable 3D displays and animations
    • Mayavi An application and library for interactive scientific data visualization and 3D plotting in Python
    • yt An open-source python package for analyzing and visualizing volumetric data
    • pandas and xarray Easy-to-use data structures and data analysis tools for Python
    • pytables and h5py Tools for using HDF5 data in Python
    • Cython and Numba Tools that allow compiled speeds in Python
    • OMFIT Software that supports integrated modeling and experimental data analysis of magnetically confined thermonuclear fusion experiments.
    • PlasmaPy An open source core Python package for plasma physics that is under development

Mathematical tools

Graphical tools

Text editing tools

  • LaTeX
    • TeXShop, complete LaTeX + BibTeX package for Mac
    • BibDesk, bibliography manager for Mac
    • LaTeXiT, compiles LaTeX formulas for presentations for Mac
    • ShareLaTeX and Overleaf, collaborative writing websites for LaTeX
    • LatexDiff, to compare different versions of a document and highlight changes
  • Emacs, powerful plain text editor
  • TextWrangler, powerful plain text editor for Mac
  • LibreOffice, office suite of programs
  • Authorea, a power collaborative writing website

See also

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