Essential software tools for the working scientist

Happy Computing

Science is more open than ever before, and part of this new openness has been both influenced and facilitated by the free software movement, including Linux. The movement around open data helps greatly with trust and reproducibility; open journals are gradually replacing the expensive and, in some ways, counter-productive traditional publishing system; and the nearly universal practice around simulation code is now to open it to the public's eyes, often on GitHub, rather than keeping it locked away in the lab's computers, treated as a trade secret.

In this environment, a proprietary OS on a scientist's desk seems out of place. I hope this very compact survey of some of what's available convinces you that you give up nothing as a scientist by adopting Linux and gain a great deal.

Infos

  1. dwm: https://dwm.suckless.org/
  2. TeX Live: https://www.tug.org/texlive/
  3. pandoc: https://pandoc.org/
  4. "Technical Writing with Pandoc and Panflute," by Lee Phillips, Linux Journal, September 2017, https://lee-phillips.org/panflute-gnuplot/
  5. gnuplot: http://gnuplot.info/
  6. "New Features in Gnuplot 5.4," by Lee Phillips, LWN, July 22, 2020, https://lwn.net/Articles/826456/
  7. LFortran: https://lfortran.org/
  8. Julia: https://julialang.org/
  9. "Fast as Fortran, Easy as Python," by Lee Phillips, ADMIN, issue 50, 2019, pg.14-19,https://www.admin-magazine.com/Archive/2019/50/Julia-Fast-as-Fortran-easy-as-Python
  10. Stefan Karpinski, "The Unreasonable Effectiveness of Multiple Dispatch," https://www.youtube.com/watch?v=kc9HwsxE1OY
  11. Oceananigans.jl: https://github.com/CliMA/Oceananigans.jl
  12. Maxima: http://maxima.sourceforge.net/
  13. SageMath: https://www.sagemath.org/
  14. "Jupyter: Notebooks for Education and Collaboration," by Lee Phillips, LWN, February, 6, 2018, https://lwn.net/Articles/746386/
  15. Bioinformatics: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/bioinformatics
  16. EMBOSS: http://emboss.open-bio.org/

The Author

Dr. Lee Phillips is a theoretical physicist and writer who has worked on projects for the Navy, NASA, and DOE on laser fusion, fluid flow, plasma physics, and scientific computation. He has written numerous popular science and computing articles and technical publications and is engaged in science education and outreach.

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