Software tools

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

• Mathics, a free alternative to Mathematica
• SymPy, symbolic calculus using Python
• Abramowitz and Stegun: Handbook of Mathematical Functions

Graphical tools

• GNUplot, also see gnuplotting.org, for producing graphs from data
• GIMP, graphics editor
• ImageJ, graphics editor and image analysis
• InkScape, vector graphics editor

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
• 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

• Digital tools for researchers
• List of revision control software