Jupyter, Mathematica, and the Future of the Research Paper

1) Binder makes that a git push away https://mybinder.org/ Want to check the discovery of gravitational waves ? Go ahead ! https://github.com/minrk/ligo-binder You know the nice thing ? it does not require you to opt-in, as long as a repo is public you an run it. So you don't need have to deploy, or know it exists. we are _already_ doing that for you.

2) Jupyter is "Just" the frontend. StackOverflow have matpltlolib, numpy, sympy, .. tags. We don't the subdomain (yet), and I actually prefer to have tags to have better searching :-)

3) Sure it's called ipywidgets (https://ipywidgets.readthedocs.io/en/latest/), that's the tech. From ipywidgets import interact, and @interact as decorator on your function... that's it.

4) For convenience Library that use ipywidgets for 3D see https://ipyvolume.readthedocs.io/en/latest/animation.html (Hey it also support VR !) See https://www.youtube.com/watch?v=nZ3HQpSXn2U that will blow your mind.

We'll try to be better at advertising our features !

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 sage, julia and everything else tied in. One text file that can be emailed around, put under version control, and can speak two dozen computer languages with babel, and has latex support for both pdf and html output.

This is a weird jab at Julia. Open source software is woefully underfunded. Julia Computing was founded in the wake of Heartbleed where people learned that open source needs some kind of funding to keep developers alive (example article: https://arstechnica.com/information-technology/2014/04/tech-... ). Coming from academic backgrounds, the core contributors really had two options if they wanted to devote full time to Julia: either everyone gets an academic job while working on Julia instead of papers (lol), or band together to get R&D funding and use that to fund a life of open source development. They did the latter.

It's quite silly to even imply there's something nefarious that can go on here. Their main product is the language. They can't sabotage that without sabotaging themselves. They may have some priorities swayed, just like how any other individual who's working on open source is doing it for their own reasons. For example, IBM funded them to add PowerPC support, and what do you know Julia works on PowerPC. Is that so awful? With this funding model, what ends up happening is you have a large group of people who dedicate their lives to developing open sourced code for automatic GPU compilation, machine learning libraries, etc. along with compiler support for optimizing scientific computing. Because of this (and other reasons), Julia ends up having a much stronger governance which is one reason why its development ends up being more active. And this activity in turn makes its project more democratic than projects like CPython or Jupyter which have been larger projects for a longer time, but with less contributors (Julia's 686 vs CPython's 524 vs Jupyter's 330).

And most of the Julia contributors aren't even part of that company! Many are academics. A lot of the funding is through NumFOCUS, a non-profit which also helps projects like Jupyter, matplotlib, etc. which the author is for! (And they are great projects as well!)

So while I am happy that the author is pro open source, I think it's necessary to point out that this open source outsider view is both wrong and dangerous. Saying that you love the purity and despise anyone who gets to make a living from it is harmful! Open source is a labor of love, but it has also destroyed many careers. I think society has this view that open source (mathematical) projects are "funded" by academic careers, but even creators of popular projects like SageMath have publicly noted that open source is harmful to academic success (https://escapethetower.wordpress.com/2016/06/13/creator-of-s...).

Instead of being against funding open source contributors, I would like to see the author promote funding for open source. Paul Romer is a leading economist. He has the power to proclaim that open source matters for academic careers and push for it to be put on equal footing with papers for grant applications in his field. People like him should be advocating for jobs dedicated to open source development, not scoffing at the supposed impurity of someone being paid to develop a public good. Someone at the top of the academic hierarchy should start a change and make the development of public tools as valued as the development of (non-public) publications.

On the other hand, open source tools are catching up. Part of the SymPy project is SymEngine which is a reconstruction in C++. SymEngine is not as feature-filled as SymPy yet, but it flies. It's much faster than SymPy, and also Mathematica. SymEngine.jl works very well since by using the symbolic types in side of Julia you get both the speed (via function specialization) while getting a lot of free features through generic code. For example, Julia code is generic over number types, so if you call inv on a matrix of SymEngine symbols the built-in Base version will compile a fast version for SymEngine symbols and use it. So you have all of Julia's Base available along with Julia packages (yeah, you can put them in a neural net if you wanted to). So SymEngine.jl is the only thing that works when I need that speed, but I do have to keep Mathematica installed for its special handling of specific equations.

And I hate to say it but... the Mathematica notebook is really pretty. You put the exponents up, the fractions on top of each other...