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Jupyter, Mathematica, and the Future of the Research Paper

paulromer.net

61–70 of 179 posts

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

#61
Right, Jupyter is nice to have, but this is really over the top nonsense:

Jupyter encourages individual integrity; Mathematica lets individuals hide behind corporate evasion

I have no idea what he's talking about re PDF export either. I print to PDF all the time, to email people a static document to look at, etc. It works just fine. (Whether you can you make book-quality formatted text easily, I've no idea, never been tempted to try.)

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

#62

Earlier quoted context omitted.

in particular I'm curious if sympy is really as good as Mathematica. I haven't used Mathematica since doing physics hw as an undergrad but it's symbolic manipulation was amazing most of the time

It's not, but for most people it may not matter. Mathematica seems to have a much larger set of integrals, differential equations, special functions, etc. that it can recognize. So as much as I dislike the language itself, I do keep Mathematica installed because in many cases SymPy cannot handle the transformation. On the other hand, open source tools are catching up. Part of the SymPy project is SymEngine which is a…

> On the other hand, open source tools are catching up.

SymPy is doing nicely, but it's decades behind Mathematica when it comes to symbolic computation.

By the way, if you want to invert a symbolic matrix, chances are that generic Gaussian elimination working with symbolic expressions isn't the best algorithm (it might even give wrong answers if zero testing is done incorrectly), and compiled code isn't going to change that. The state of the art in symbolic linear algebra uses specialized algorithms like evaluation-interpolation, modular computation, and all kinds of low level optimizations.

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

#63
post #41

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 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…

Science publication is moving (very, very, very slowly) towards a model where instead of a final, polished traditional paper, the raw data along with the software tools and interpretation is published. In principle this should allow readers to completely understand and reproduce the processing of the raw data, rather than reading a few paragraphs summarizing the processing done by the authors. Using a closed source tool for processing the data limits how deeply a reader can delve into the processing that the authors did, because the functions in the proprietary package are black boxes. Jupyter has no black boxes.

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

#64

Earlier quoted context omitted.

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.

I think your estimate of 99% is a wee bit high. At least in the field I'm familiar with, astronomy, the idea of using Excel for any serious computation or design would be met with laughter.

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

#65
post #52

Jupyter is an amazing and useful piece of software. I agree that its openness is important, that its flexibility in producing content is excellent, and that it deserves to be the current hotness. But I'm afraid > Now, Jupyter is the unambiguous technical leader. is pure fantasy, imho. SymPy is still two decades behind Mathematica in large swathes of symbolic computation. It may be that, for the things that the author…

[deleted]

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

#66
post #41

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 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…

Science publication is moving (very, very, very slowly) towards a model where instead of a final, polished traditional paper, the raw data along with the software tools and interpretation is published. In principle this should allow readers to completely understand and reproduce the processing of the raw data, rather than reading a few paragraphs summarizing the processing done by the authors. Using a closed source t…

In principle this should allow readers to completely understand and reproduce the processing of the raw data, rather than reading a few paragraphs summarizing the processing done by the authors. Using a closed source tool

But consider http://www.bbc.co.uk/news/science-environment-39054778

"Science is facing a "reproducibility crisis" where more than two-thirds of researchers have tried and failed to reproduce another scientist's experiments"

I don't think that can be handwaved away as "OMG closed source software!". Especially since all the scientists in a given field will have access to the same software anyway. Give them open source and the issue will persist, and we both know it because the root cause isn't anything to do with the license of the software

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

#67
post #61

Right, Jupyter is nice to have, but this is really over the top nonsense: Jupyter encourages individual integrity; Mathematica lets individuals hide behind corporate evasion I have no idea what he's talking about re PDF export either. I print to PDF all the time, to email people a static document to look at, etc. It works just fine. (Whether you can you make book-quality formatted text easily, I've no idea, never bee…

I suspect that the OP used the "Print..." command in the File menu, and selected PDF as the printer option. ISTR that this can sometimes result in poor quality results as presumably it is relying on an external PDF engine to render the notebook.

Whenever I've used the "Save As..." command, choosing PDF as the target, I've also only had good quality output.

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

#68
post #37
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…

Has anyone tried integrating this sort of thing into LibreOffice? I bet Calc would make a decent DataFrame tool.

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

#70
post #14
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…

> it's free Well for you maybe – and we strongly believe it should be – but it's built on top of thousand of volunteers hours, grants money (Thanks Sloan, Helmsley, Moore) and donation from companies (Anaconda, microsoft...) and individual, and partners. NumFOCUS ( https://www.numfocus.org/ ) manage all of that it's a 501c3 tax deductible ! If Jupyter is of help to you (or your company, organisation) think about cont…

I can only imagine how many billions of dollars in company value have been generated using the product of their uncompensated labor.

Same goes for the rest of the data stack: Python itself, Numpy, Scipy, Scikit-Learn, Pandas, etc.

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