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.

« Previous 1 2 3

Buy this article as PDF

Express-Checkout as PDF
Price $2.95
(incl. VAT)

Buy Linux Magazine

SINGLE ISSUES
Print Issues
Digital Issues
 
SUBSCRIPTIONS
Print Subs
Digisubs
 
TABLET & SMARTPHONE APPS
Get it on Google Play

US / Canada

Get it on Google Play

UK / Australia

Related content

  • Maxima

    This free algebra tool helps you keep ahead of the calculations.

    more »
  • Brave GNU World

    This column looks into projects and current affairs in the world of free software from the perspective of the GNU Project and the FSF. In this issue, I’lll focus on Comspari and the EU decision on software patents.

    more »
  • Swiss Army Knife

    Pandoc lets you convert files from one markup format to another at the command line.

    more »
  • Julia

    Parallel processing is indispensable today – particularly in the field of natural sciences and engineering. Normal desktop users, however, can also benefit from higher performance through parallel execution with at least four calculation cores.

    more »
  • KDE SC 4.4

    Version 4.4 sees the KDe Software Compilation reach a status on par with the user friendliness and stability of good old KDe 3.5. On top of this, many features are new.

    more »
comments powered by Disqus

Visit Our Shop

Trial Subscription

Digital Subscription

Subscribe

Direct Download

Read full article as PDF:

Price $2.95

News

Tag Cloud

Administration Community Desktop Events Hardware Linux Linux Pro Magazine Mobile Programming Software Ubuntu Web Development Windows free software open source