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Over at the Linux Journal, Glyn Moody writes about how the tradition of open science implies a call for the use of Open-Source Software. He notes that even in the first issue of the Royal Society's Philosophical Transactions, which is the oldest scientific journal in continuous publication in the world, the principles for open science are taken as a given. Thus, he explains how open source software, along with both Open Data and Open Access publication, should be a natural fit for scientific work.
When did open source begin? In February 1998, when the term was coined by Christine Peterson? Or in 1989, when Richard Stallman drew up the "subroutinized" GNU GPL? Or perhaps a little earlier, in 1985, when he created the GNU Emacs license? How about on March 6, 1665? On that day, the following paragraph appeared:
Whereas there is nothing more necessary for promoting the improvement of Philosophical Matters, than the communicating to such, as apply their Studies and Endeavours that way, such things as are discovered or put in practise by others; it is therefore thought fit to employ the Press, as the most proper way to gratifie those, whose engagement in such Studies, and delight in the advancement of Learning and profitable Discoveries, doth entitle them to the knowledge of what this Kingdom, or other parts of the World, do, from time to time, afford, as well of the progress of the Studies, Labours, and attempts of the Curious and learned in things of this kind, as of their compleat Discoveries and performances: To the end, that such Productions being clearly and truly communicated, desires after solid and usefull knowledge may be further entertained, ingenious Endeavours and Undertakings cherished, and those, addicted to and conversant in such matters, may be invited and encouraged to search, try, and find out new things, impart their knowledge to one another, and contribute what they can to the Grand design of improving Natural knowledge, and perfecting all Philosophical Arts, and Sciences.
Much more could be done by scientific funding bodies to benefit from Open Source Software, while at the same time many Open Source Software projects could do better in reaching out to the scientific community.
(Score: 2) by FatPhil on Thursday December 06 2018, @04:57AM (6 children)
Yes, hockey sticks, I'm thinking of you.
Whether open source software satisfies those requirements better than closed source software is a completely separate argument, and given that emacs on my dev machine segfaults about once a week, is one that has no clear conclusion. Sure, it has the potential o be better, and opportunities to improve it are unfettered, but what really matters is if that potential is realised, right now, when I need to use it to analyse the scientist's data.
The smartest scientists, the ones probably doing the best work, are probably smart enough to work out what are the best tools for the job, right now - which is when they need it. Nobody should dictationg what software they use: firstly the invisible hand will guide them, and secondly, we should trust them to work out what helps them do science best.
Great minds discuss ideas; average minds discuss events; small minds discuss people; the smallest discuss themselves
(Score: 4, Interesting) by richtopia on Thursday December 06 2018, @07:18AM (1 child)
Yes. In my limited experience researching at the university there was typically two motivating factors to what software to use: 1. Does the researcher already know it? and 2. The price (assuming rough feature compatibility). Inherently, open source software is present as it is much easier to download and get using open source software than it is to get approval from someone to purchase commercial software.
Now, I don't want to set the expectation that researchers should be contributing code or donating fast sums of money to projects. Most researchers with the proper qualifications already host their code on Git Hub, so the remaining researchers are people like me, who at best write simple python scripts to automate tasks. And looking at financial donations: if you think getting approval to purchase software is difficult, image how difficult it is to donate software. Best case I could see a bounty or intern hire to write specific functionality, but once again the work is deviating from the real goals of the research project.
(Score: 0) by Anonymous Coward on Friday December 07 2018, @09:37PM
Psst. The word is vast.
(Score: 1) by shrewdsheep on Thursday December 06 2018, @01:07PM (1 child)
What should be open source is not so much the base software used to perform well-defined analyses/tasks. Others pointed out that it is more important to document and test the base software than being open. It is much more important to have the analysis script/program of the researcher being open (reproducible science) as this is what the researcher did in place of what he said.
That being said open source can be a huge catalytic factor for science. One example is the R eco-system. R is the leading statistical environment by far at the moment dwarfing all commercial competitors. One big factor is that good statisticians are often bad programmers. What they can do is copy-paste an existing package, make their modification and make it available as a new package. If a package is really important after some time a capable programmer will re-implement it nicely and modular.
(Score: 2) by FatPhil on Friday December 07 2018, @04:02AM
Great minds discuss ideas; average minds discuss events; small minds discuss people; the smallest discuss themselves
(Score: 0) by Anonymous Coward on Thursday December 06 2018, @06:05PM
"But none o that analysis *needs*, morally, to be done using open source software,"
the hell it doesn't. these institutions should be using and donating/contributing to Free Software. using proprietary shit with public dollars or even (moral) private dollars is conspiracy to defraud, and makes these institutions complicit in the digital slave trade.
(Score: 3, Interesting) by choose another one on Thursday December 06 2018, @06:15PM
This.
But I would go a bit further - when verifying / replicating scientific research it is actually vitally important to _not_ use the same tools as the authors, so if you are an open-source proponent and the author used Excel, then great - you use an open source spreadsheet, if you can't replicate _then_ you can investigate if the science is wrong or your tool is wrong or the researchers tool is wrong. If you use the same tool as the author, whether it's open source, closed source, or the author's custom written tool, you are _not_ properly verifying the science, a fault in the tool may mean the it is bunk.
This isn't a theoretical concern, when I was in research Intel came out with the Pentium, totally awesome bang-for-buck, loads of researchers used it, then FDIV bug was found and boy was there a lot of panic from people trying to port stuff to run on other machines (Unix boxen mostly - nothing else had the same power) or run stuff on other machines, other machines which got real busy real quick. There were people I knew whose results were indeed different when run on Pentium and more-correct machines, but everyone had to check in case.
If the Pentium had been an open-source processor that everyone was required to use, the FDIV bug might never have been spotted. Same goes for software tools.