The Scientific Paper Is Obsolete. Here's What's Next. - The Atlantic


110 bookmarks. First posted by farley13 april 2018.


The paper announcing the first confirmed detection of gravitational waves was published in the tr
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9 days ago by flowscape
Brilliant article juxtaposing Mathematica and Jupyter:
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7 weeks ago by wspr
Missed this - all about the origin of Jupyter Notebooks, in - awesome article.
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8 weeks ago by macloo
In a compelling story for The Atlantic, James Somers argued that Jupyter notebooks may replace the traditional research paper typically shared as a PDF.
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8 weeks ago by gwijthoff
But it’s hard to sell the scientific community on a piece of commercial software. Even though Wolfram Research has given away a free Mathematica notebook viewer for years, and even though most major universities already have a site license that lets their students and faculty use Mathematica freely, it might be too much to ask publishers to abandon PDFs, an open format, for a proprietary product. “Right now if you make a Mathematica notebook and you try to send that to a journal,” Gray says, “they’re gonna complain: Well, we don’t have Mathematica, this is an expensive product—give us something that’s more of a standard.”

“At this point, nobody in their sane mind challenges the fact that the praxis of scientific research is under major upheaval,” Pérez, the creator of Jupyter, wrote in a blog post in 2013. As science becomes more about computation, the skills required to be a good scientist become increasingly attractive in industry. Universities lose their best people to start-ups, to Google and Microsoft. “I have seen many talented colleagues leave academia in frustration over the last decade,” he wrote, “and I can’t think of a single one who wasn’t happier years later.”

Pérez told me stories of scientists who sacrificed their academic careers to build software, because building software counted for so little in their field: The creator of matplotlib, probably the most widely used tool for generating plots in scientific papers, was a postdoc in neuroscience but had to leave academia for industry. The same thing happened to the creator of NumPy, a now-ubiquitous tool for numerical computing. Pérez himself said, “I did get straight-out blunt comments from many, many colleagues, and from senior people and mentors who said: Stop doing this, you’re wasting your career, you’re wasting your talent.” Unabashedly, he said, they’d tell him to “go back to physics and mathematics and writing papers.”
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8 weeks ago by craniac
Surprisingly deep exploration. See also next post.
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august 2018 by jgordon
The Scientific Paper Is Obsolete
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june 2018 by jhfrudd
clickbaity headline, but some interesting stuff about Wolfram and Jypiter - The Scientific Paper Is Obsolete
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june 2018 by puja
On the rise of interactive notebooks for teaching through exploration. Starts with Bret Victor, then meanders into Jupyter vs Mathematica. Ignores Hypercard, Nicky Case.
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may 2018 by gerwitz
Jupyter, Mathematica, computable documents
mathematica  python  science 
may 2018 by pgt150
PNAS / Richard Goerg / Getty / The Atlantic T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed…
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april 2018 by leftyotter
The grand scientific challenges of our day are as often as not computational puzzles: How to integrate billions of base pairs of genomic data, and 10 times that amount of proteomic data, and historical patient data, and the results of pharmacological screens into a coherent account of how somebody got sick and what to do to make them better? How to make actionable an endless stream of new temperature and precipitation data, and oceanographic and volcanic and seismic data? How to build, and make sense of, a neuron-by-neuron map of a thinking brain? Equipping scientists with computational notebooks, or some evolved form of them, might bring their minds to a level with problems now out of reach.
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april 2018 by pwhaley
The Scientific Paper Is Obsolete. Here's What's Next. – The Atlantic
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april 2018 by jackysee
The origins of Jyupiter
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april 2018 by traggett
The Scientific Paper Is Obsolete Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. Added April 19, 2018 at 04:50PM
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april 2018 by np
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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april 2018 by kintopp
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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april 2018 by indirect
It’s Apple v. Microsoft all over again, only this time Linux is winning
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april 2018 by miljko
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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april 2018 by johnrclark
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
april 2018 by jkleske
The 1988 Forbes profile about him tried to get to the root of it: “In the words of Harry Woolf, the former director of the prestigious Institute for Advanced Study in [Princeton, New Jersey]—where Wolfram, at 23, was one of the youngest senior researchers ever—he has ‘a cultivated difficulty of character added to an intrinsic sense of loneliness, isolation, and uniqueness.’” But where Mathematica gets its powers from an army of Wolfram Research programmers, Python’s bare-bones core is supplemented by a massive library of extra features—for processing images, making music, building AIs, analyzing language, graphing data sets—built by a community of open-source contributors working for free. Instead of building a specialized, stand-alone application, let alone spending man-centuries on it, the IPython team—Pérez was now joined by Brian Granger, a physics professor at California Polytechnic State University at San Luis Obispo; and Min Ragan-Kelley, a Ph.D. student at UC Berkeley working in computational physics—built their notebooks as simple web pages. “I’m all in favor of there being a maniac in the middle.”A 1997 essay by Eric S. Raymond titled “The Cathedral and the Bazaar,” in some sense the founding document of the modern open-source movement, challenged the notion that complex software had to be built like a cathedral, “carefully crafted by individual wizards or small bands of mages working in splendid isolation.” Raymond’s experience as one of the stewards of the Linux k
april 2018 by sechilds
At every turn, IPython chose the way that was more inclusive, to the point where it’s no longer called “IPython”: The project rebranded itself as “Jupyter” in 2014 to recognize the fact that it was no longer just for Python. The Jupyter notebook, as it’s called, is like a Mathematica notebook but for any programming language. You can have a Python notebook, or a C notebook, or an R notebook, or Ruby, or Javascript, or Julia. Anyone can build support for their programming language in Jupyter. Today it supports more than 100 languages.

Theodore Gray, who developed the original Mathematica notebook interface, said that he once as an experiment tried to build support for other programming languages into it. “It never went anywhere,” he told me. “The company had no interest in supporting this. And also because when you have to support a lot of different languages, you can’t do it as deeply.”
mathematica  jupyper  python  science  research 
april 2018 by euler
“Scientific methods evolve now at the speed of software; the skill most in demand among physicists, biologists, chemists, geologists, even anthropologists and research psychologists, is facility with programming languages and “data science” packages. ” https://t.co/mrBC5TR0dD pic.twitter.com/sE8zlw7FJr

— Will Richardson (@willrich45) April 11, 2018
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april 2018 by willrichardson
I adore this piece about scientific papers becoming obselete. Computers! Drama! Big dumb personalities!
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april 2018 by robinrendle
a cultivated difficulty of character added to an intrinsic sense of loneliness, isolation, and uniqueness

S. Wolfram is E. Yudkowsky if Yudkowsky actually were as intelligent and accomplished as he thinks.

[and Wolfram himself is such a gigantic ass that every article about his products and achievements ends up getting digressing on what an ass he is.]
science  publishing  tech  wolfram 
april 2018 by tkmharris
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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april 2018 by bschlagel
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
from instapaper
april 2018 by joeywu02
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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april 2018 by joostw
Slow-paced & inefficient, can research journals adapt to keep up with the pace of change?
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april 2018 by mathewi
Slow-paced & inefficient, can research journals adapt to keep up with the pace of change?
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april 2018 by fkbarrett
“Elsevier hired me to do some consulting thing about ‘What would the future of scientific publishing look like?’” This was before the Mathematica notebook, but he gave them a spiel along the same lines. “A few years ago I was talking to some of their upper management again. I realized in this meeting, oh my gosh, I said exactly the same things 35 years ago!”
The paper announcing the first confirmed detection of gravitational waves was published in the traditional way, as a PDF, but with a supplemental IPython notebook. The notebook walks through the work that generated every figure in the paper. Anyone who wants to can run the code for themselves, tweaking parts of it as they see fit, playing with the calculations to get a better handle on how each one works. At a certain point in the notebook, it gets to the part where the signal that generated the gravitational waves is processed into sound, and this you can play in your browser, hearing for yourself what the scientists heard first, the bloop of two black holes colliding.
At every turn, IPython chose the way that was more inclusive, to the point where it’s no longer called “IPython”: The project rebranded itself as “Jupyter” in 2014 to recognize the fact that it was no longer just for Python. The Jupyter notebook, as it’s called, is like a Mathematica notebook but for any programming language.
When you improve the praxis of science, the dream is that you’ll improve its products, too. Leibniz’s notation, by making it easier to do calculus, expanded the space of what it was possible to think. The grand scientific challenges of our day are as often as not computational puzzles: How to integrate billions of base pairs of genomic data, and 10 times that amount of proteomic data, and historical patient data, and the results of pharmacological screens into a coherent account of how somebody got sick and what to do to make them better? How to make actionable an endless stream of new temperature and precipitation data, and oceanographic and volcanic and seismic data? How to build, and make sense of, a neuron-by-neuron map of a thinking brain? Equipping scientists with computational notebooks, or some evolved form of them, might bring their minds to a level with problems now out of reach.
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april 2018 by rauschen
T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated…
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april 2018 by matttrent
The Scientific Paper Is Obsolete | T he scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated… | https://ift.tt/2JmUaob | via Instapaper and IFTTT
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april 2018 by habi
The idea for IPython’s notebook interface came from Mathematica. Pérez admired the way that Mathematica notebooks encouraged an exploratory style. “You would sketch something out—because that’s how you reason about a problem, that’s how you understand a problem.” Computational notebooks, he said, “bring that idea of live narrative out ... You can think through the process, and you’re effectively using the computer, if you will, as a computational partner, and as a thinking partner.”

Instead of building a specialized, stand-alone application, let alone spending man-centuries on it, the IPython team—Pérez was now joined by Brian Granger, a physics professor at California Polytechnic State University at San Luis Obispo; and Min Ragan-Kelley, a Ph.D. student at UC Berkeley working in computational physics—built their notebooks as simple web pages. The interface is missing Mathematica’s Steve Jobsian polish, and its sophistication. But by latching itself to the web, IPython got what is essentially free labor: Any time Google, Apple, or a random programmer open-sourced a new plotting tool, or published better code for rendering math, the improvement would get rolled into IPython. “It has paid off handsomely,” Pérez said.

The paper announcing the first confirmed detection of gravitational waves was published in the traditional way, as a PDF, but with a supplemental IPython notebook. The notebook walks through the work that generated every figure in the paper. Anyone who wants to can run the code for themselves, tweaking parts of it as they see fit, playing with the calculations to get a better handle on how each one works. At a certain point in the notebook, it gets to the part where the signal that generated the gravitational waves is processed into sound, and this you can play in your browser, hearing for yourself what the scientists heard first, the bloop of two black holes colliding.
science  publishing  mathematica  python 
april 2018 by madamim
This is, of course, the whole problem of scientific communication in a nutshell: Scientific results today are as often as not found with the help of computers. That’s because the ideas are complex, dynamic, hard to grab ahold of in your mind’s eye. And yet by far the most popular tool we have for communicating these results is the PDF—literally a simulation of a piece of paper. Maybe we can do better.
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april 2018 by zryb
RT : adroitly connects 's Explorable Explanations, 's Mathematica, an…
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april 2018 by mshook
Ready to move to the next artefact to disseminate science... Let's all go to Jupyter
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april 2018 by shaneisley
adroitly connects 's Explorable Explanations, 's Mathematica, an…
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april 2018 by kleinsound
adroitly connects 's Explorable Explanations, 's Mathematica, an…
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april 2018 by grantpotter
Here’s what’s next. The scientific paper—the actual form of it—was one of the enabling inventions of modernity. Before it was developed in the 1600s, results were communicated privately in letters, ephemerally in lectures, or all at once in books. via Pocket
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april 2018 by archizoo
A very nice essay on the nature and format of the scientific manuscript:
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april 2018 by cdrago
RT : The Scientific Paper Is Obsolete
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april 2018 by freerange_inc