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Jupyter, Mathematica, and the Future of the Research Paper

paulromer.net

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Re: Jupyter, Mathematica, and the Future of the Research Paper

#41

Post by gaius »

askvictor wrote: post #27
FractalLP wrote: post #23

Long time user of Python here and recent user of Mathematica. Some observations I have are that they're both great. Python is a nice open source scripting language, but getting libraries to work can sometimes be a pain. Mathematica is basically install this and everything is included. The Mathematica documentation is amazing and it is really simple how to do most things. The whole iPhone "there is an app for that" is…

While I totally hear you regarding the pain of python modules (particularly on Windows), the point of python 'distributions' like anaconda and canopy is to bring the kitchen sink along, kind of like mathematica. The problem with Mathematica from a science point of view is that, being closed source, means you can't independently ensure the calculations are happening correctly. To be replicable, science involving data…

The problem with Mathematica from a science point of view is that, being closed source, means you can't independently ensure the calculations are happening correctly

Have there been any high profile failures root-caused to Mathematica (or MATLAB or any similar product) getting its sums wrong? I can find any news stories etc. Plenty of serious calculations were and are done on “closed source” HP and TI calculators too. Every serious scientific instrument with its own data capture uses a binary blob too somewhere, so if that’s a problem for you then you can’t even trust the raw data!

And even if you have all of the code - you still need to worry if the proprietary, closed FPU is working “correctly”.

This sounds very much like a post-hoc justification for “its free as in beer”. Do you think Wikipedia is more trustworthy than real references too? What about blogs?

Re: Jupyter, Mathematica, and the Future of the Research Paper

#42

Post by williamstein »

zeth___ wrote: post #31
williamstein wrote: post #24

Earlier quoted context omitted.

Thanks for mentioning SageMath and CoCalc (I founded both of these projects)! A minor clarification is that CoCalc is not a rebranding of SageMath, but is instead a new web application whose goal is to make it very easy to collaboratively use Sage, Jupyter, LaTeX, Julia, etc. In constract, Sage is a more traditional open source software package, which people install on their own computers. The goal of Sage is to be a…

Have you had a look at org-mode babel? It's extremely interesting how they have managed to create an all plain text environment that is in some ways[0] better than the current notebooks. Of course it's not as user friendly and needs quite a bit of polish, and a major refactor to separate the above use case from the tangle use case. The tangle part of org is even more interesting as it's probably the first fully liter…

Yes, org-mode is very inspiring. But, as you say, it's not quite user friendly enough for some target audiences (e.g., beginning students).

Re: Jupyter, Mathematica, and the Future of the Research Paper

#43

Post by falkod »

askvictor wrote: post #30

I'm surprised there's no mention or discussion of the importance of open-source tooling for replicable science. Without seeing and reviewing the source, how can you tell that a particular calculation is right? Also, relying on costly tools such as Mathematica cuts off a sizable amount of the population from being able to replicate or play with your findings on cost grounds alone.

Long-term Mathematica user (physicist) here: I don't think the use of open source software would make most science -- maybe that does not apply to cs/datascience -- more replicable. Usually that takes an expert in the field. And usually these experts are employed at universities where Mathematica licenses are not the prime cost factor. That said, I am all for open source software. Although I would argue that probably trustable scientific results do not rely on the inner workings of e.g. Mathematica anyway, but use Mathematica as vehicle for say linear algebra or symbolic manipulation etc. While the inner workings of Mathematica may not be open source, in principle the relevant algorithms are not propriertary but usually well-known mathematical results and as such at least in principle easily reproducible outside of the ecosystem.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#44

Post by dEnigma »

gaius wrote: post #38
cs702 wrote: post #2

This is spot-on: "Membership in an open source community is like membership in the community of science. There is a straightforward process for finding a true answer to any question. People disagree in public conversations. They must explain clearly and listen to those who response with equal clarity. Members of the community pay more attention to those who have been right in the past, and to those who enhance their…

Membership in an open source community is like membership in the community of science. There is a straightforward process for finding a true answer to any question Oh please. Dare to ask what is the best of anything and prepare for an epic flame war.

Because "What is the best X" is a vague question and rarely has just one true answer.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#45

Post by gaius »

dEnigma wrote: post #44
gaius wrote: post #38

Earlier quoted context omitted.

Membership in an open source community is like membership in the community of science. There is a straightforward process for finding a true answer to any question Oh please. Dare to ask what is the best of anything and prepare for an epic flame war.

Because "What is the best X" is a vague question and rarely has just one true answer.

As is true of most interesting questions in most fields.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#46

Post by dEnigma »

gaius wrote: post #45
dEnigma wrote: post #44

Earlier quoted context omitted.

Because "What is the best X" is a vague question and rarely has just one true answer.

As is true of most interesting questions in most fields.

Possibly, but this is why one shouldn't expect to get a simple, "true" answer or be suprised when there are arguments and flamewars.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#47

Post by sanderjd »

gaius wrote: post #37
dahart wrote: post #8

> The tie-breaker is social, not technical. The tie-breaker is financial. Jupyter is winning because it's free, not because it's social. It becomes social because of widespread adoption, and it get's widespread adoption because it's free. I love Jupyter, love love love. But there's a lot of hyperbole and opinion here. Mathematica is just a for-profit business, it's that simple. And it wouldn't be fair to deny the exa…

The tie-breaker is financial. Jupyter is winning because it's free This is it really Back in the 90s I was using a program called MathCAD, it provided a “notebook” interface by running as a plugin to Word 6. In terms of general usability and experience, 20-years-ago blows away modern-day Jupyter and it’s silly “cells” interface, which it does not because it’s better but because it’s trying to force itself into a web…

I used MathCAD in physics and chemistry classes in college. I frequently wonder what happened to it, because I share your perception that while Jupyter is very nifty, it is hamstrung by the limitations of the browser environment.

I'm waiting impatiently for the coming revolution of non-web collaborative internet-connected rich client applications.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#48

Post by inigoalonso »

starpilot wrote: post #40
askvictor wrote: post #27

Earlier quoted context omitted.

While I totally hear you regarding the pain of python modules (particularly on Windows), the point of python 'distributions' like anaconda and canopy is to bring the kitchen sink along, kind of like mathematica. The problem with Mathematica from a science point of view is that, being closed source, means you can't independently ensure the calculations are happening correctly. To be replicable, science involving data…

> The problem with Mathematica from a science point of view is that, being closed source, means you can't independently ensure the calculations are happening correctly. To be replicable, science involving data needs to use open source tools. Excel and MATLAB can't be used for real science?

At least you need to be very careful with them: https://genomebiology.biomedcentral.com/articles/10.1186/s13...

Abstract: "The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions."

Re: Jupyter, Mathematica, and the Future of the Research Paper

#49

Post by starpilot »

inigoalonso wrote: post #48
starpilot wrote: post #40

Earlier quoted context omitted.

> The problem with Mathematica from a science point of view is that, being closed source, means you can't independently ensure the calculations are happening correctly. To be replicable, science involving data needs to use open source tools. Excel and MATLAB can't be used for real science?

At least you need to be very careful with them: https://genomebiology.biomedcentral.com/articles/10.1186/s13... Abstract: "The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene…

Yeah, but that doesn't change the fact that 99% of the science/engineering/business world is reliant on Excel. Airplanes are designed in Excel.

Re: Jupyter, Mathematica, and the Future of the Research Paper

#50

Post by tincholio »

sanderjd wrote: post #47
gaius wrote: post #37

Earlier quoted context omitted.

The tie-breaker is financial. Jupyter is winning because it's free This is it really Back in the 90s I was using a program called MathCAD, it provided a “notebook” interface by running as a plugin to Word 6. In terms of general usability and experience, 20-years-ago blows away modern-day Jupyter and it’s silly “cells” interface, which it does not because it’s better but because it’s trying to force itself into a web…

I used MathCAD in physics and chemistry classes in college. I frequently wonder what happened to it, because I share your perception that while Jupyter is very nifty, it is hamstrung by the limitations of the browser environment. I'm waiting impatiently for the coming revolution of non-web collaborative internet-connected rich client applications.

As a die-hard Emacs user, I think that org-mode with it's org-babel capabilities blows Jupyter out of the water, and it produces much better, readable output. You can use it with pretty much any language, and combine several languages in a single document without any issues. Besides all this, it's just a plain text format, and you can extract all the code into proper source files for later offline use, too ('tangling', in literate programming parlance). Jupyter uses a rather obtuse json format which is not practical to work on directly.

Of course, it's not web-based and it requires some basic knowledge of Emacs, but functionality-wise is so much better that it ends up being frustrating to use Jupyter when collaborating with other people. There are some workarounds (EIN, and ob-ipython modes help, but it's not quite the same)

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