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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

#31

Post by zeth___ »

williamstein wrote: post #24
zeth___ wrote: post #13

Jupyter isn't a foil for mathematica. It has completely different use cases. The straight one to one fight is between sagemath, or their rebranded cocal site, and mathematica. In terms of ability to do things sagemath is the glue between all the amazing open source math and science software that has been written over the last 50 years. https://cocalc.com/ But in terms of presentation by far the best is org-mode with…

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 literate system that allows you to completely document everything about a software project. And since it's language agnostic I do mean everything from install, compile, connect to the external databases, export the documentation in every format under the sun and whatever else you can think of (including docx through pandoc).

I'm going through the source code slowly to get it streamlined, but the code is suffering from the typical lisp syndrome of "Everything is implemented everywhere."

[0] Being able to run multiple languages on the same org file, controlling environments for scripting languages, compiling on page for non-scripting languages.

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

#32

Post by sonofaragorn »

ILikeConemowk wrote: post #15
carreau wrote: post #14

Earlier quoted context omitted.

> 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…

Fernando, the creator of Ipython and ultimately what morphed into Jupyter is missing from your list. That dude is an inspiration.

Thank you for mentioning him, I didn't know of him. For anyone interested here is an interesting talk he gave recently: https://www.youtube.com/watch?v=xuNj5paMuow

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

#34

Post by stjohnswarts »

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…

Exactly, you can be a programmer and be a capitalist too. May the best paradigm or hybrid of the various paradigms win.

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

#35

Post by chillydawg »

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…

I'm not sure I agree with that. If you publish your methods and make your data available, then a replicator has all they need. They'd have to reimplement the data pipeline anyway, otherwise it's not a replicated result it's just someone running your notebook with potentially the same bugs in it again.

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

#36

Post by llamaz »

wodenokoto wrote: post #33

Since the author is talking about using Jupyter for research papers, how do you do basic things, like bibliographies, naming tables and referencing them later? I have seen table of content, but those have been generated by a big block of javascript.

You can export to LaTeX and hack the "template" (in the terminology of Jupyter) that defines how this conversion occurs.

I used this as a starting point and modified it for my own purposes: http://blog.juliusschulz.de/blog/ultimate-ipython-notebook

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

#37

Post by gaius »

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 browser. I haven’t used MathCAD since but I bet in 2018 it’s amazing.

I think few people who have used the commercial tools think Jupyter is better. But the commercial tools are soooooooo expensive...

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

#38

Post by gaius »

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.

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

#39

Post by gaius »

askvictor wrote: post #28
yaroslavvb wrote: post #9

I've been using Mathematica since 1995 and Jupyter/colab for 5+ years. Most recently I've been using them both in parallel. While Jupyter is probably the future in terms of mass adoption, there are still some areas where Jupyter is lagging. 1. Mathematica has an easy way of sharing notebook. I just run "deploy" command which turns notebook into publicly accessible webpage, hosted by wolfram, here's an example -- http…

With regards to sharing, both Google and Microsoft have free hosting for shareable jupyter notebooks. Probably not quite as easy to get them from your computer to the cloud as a deploy command, but it probably wouldn't be hard to create a module that does exactly that (if one doesn't already exist)

See https://blogs.msdn.microsoft.com/uk_faculty_connection/2017/... - you can easily import from Github

https://notebooks.azure.com

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

#40

Post by starpilot »

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. To be replicable, science involving data needs to use open source tools.

Excel and MATLAB can't be used for real science?

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