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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

#121

Post by TeMPOraL »

EGreg wrote: post #97

It always goes like this. The initial solutions may be proprietary, and financed by investors. They have a business model so of course they don’t give everything away for free. With time, enough people get together to build an open source alternative. And then like a snowball it eclipses everything proprietary that went before it. What would a world look like that didn’t apply Capitalism to ideas? One where companies…

> It always goes like this.

> The initial solutions may be proprietary, and financed by investors. They have a business model so of course they don’t give everything away for free.

> With time, enough people get together to build an open source alternative. And then like a snowball it eclipses everything proprietary that went before it.

I wish it did. The most obvious counterexamples that come to mind are Microsoft Office and Adobe Photoshop. With maybe the recent exception of Krita for the latter case, there are no known open-source alternatives that don't suck hard compared to the propertiary applications I mentioned.

I'm not really sure why that happens, but open source doesn't seem to scale well when building large end-user applications.

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

#122

Post by jononor »

tincholio wrote: post #108
dahart wrote: post #103

Earlier quoted context omitted.

> What I wonder is why are Jupyter notebooks so popular? How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Think about the recipients rather than how hard it is for you. Assume the person you share with needs to be able to re-run your notebook. Assume the person you share with isn't using the same operating system that you are. Be honest and think about all the steps i…

> How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Well, now you're talking about a whole environment. Use docker, or VMs or whatever. There's plenty of options for doing this (we actually use Docker for Jupyter, to make sure we work off a consistent install, so I guess sharing can be non-trivial if you walk a bit off the beaten path, anyway) > If I choose to use a di…

There are Jupyter kernels for most languages out there. https://github.com/jupyter/jupyter/wiki/Jupyter-kernels

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

#123

Post by dahart »

tincholio wrote: post #108
dahart wrote: post #103

Earlier quoted context omitted.

> What I wonder is why are Jupyter notebooks so popular? How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Think about the recipients rather than how hard it is for you. Assume the person you share with needs to be able to re-run your notebook. Assume the person you share with isn't using the same operating system that you are. Be honest and think about all the steps i…

> How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Well, now you're talking about a whole environment. Use docker, or VMs or whatever. There's plenty of options for doing this (we actually use Docker for Jupyter, to make sure we work off a consistent install, so I guess sharing can be non-trivial if you walk a bit off the beaten path, anyway) > If I choose to use a di…

Yes, Anaconda + Jupyter is an environment and org mode is not. That’s a big reason Jupyter is so popular.

> I don’t get your point.

My point was Jupyter inflicts far less technical burden and debt on other people. There’s a huge downside to custom environments. If that’s not obvious, that explains why it’s hard to understand jupyter’s popularity.

> it requires a minimum of computer literacy

I’m sure you didn’t mean it that way, but this borders on white tower programmer centric dismissiveness.

Personally I know how to install all the things an org mode notebook might require, but I don’t want to. It takes too much of my time and energy. Expecting other people to adopt your choice of tools and environment by arguing that your tools are basic literacy is presumptuous. Use org mode, I’m wildly in favor of people using tools that they like, and you like it. Just don’t claim it’s objectively better on all axes when it’s not.

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

#124

Post by takluyver »

dahart wrote: post #103
todd8 wrote: post #92

Earlier quoted context omitted.

I share your opinion about the superiority of org-mode as a means to assemble a document out of various pieces. It's not hard to show nicely formatted code, the code's output, the math behind the code and perhaps a graph of the results all in a LaTeX/PDF document and or HTML. All of this can be done with a flat text file that is easy to save as a part of a project under source control. What I wonder is why are Jupyte…

> What I wonder is why are Jupyter notebooks so popular? How easy is it to share a Jupyter notebook with someone else, versus sharing an org-mode notebook? Think about the recipients rather than how hard it is for you. Assume the person you share with needs to be able to re-run your notebook. Assume the person you share with isn't using the same operating system that you are. Be honest and think about all the steps i…

If the notebook is something you can share publicly, then https://mybinder.org/ makes sharing even easier. You send a link, and the only thing the recipient needs is a modern browser.

If they want to actually work on the notebook and keep their changes, they'll probably need to install it (or switch to a platform like Cocalc). But Binder is enough to let them view, run it and make experimental changes, without installing anything or creating any new account.

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

#125

Post by madengr »

gaius wrote: post #41
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 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…

I’ll add that many closed sourced developers will show you sections of the source code if you sign an NDA. I’ve done that on several occasions when I needed to see how a model was implemented. As long as you are not a competitor, it’s usually not an issue. I sign NDAs often to see IP.

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

#126

Post by dahart »

tincholio wrote: post #106
dahart wrote: post #96

Earlier quoted context omitted.

I Agree with all those points. I've used org mode for a few things, but not for python notebooks. I remember seeing a great video a few years back on using python in org mode to make a research notebook. It really made me want to try org mode for literate / notebook style programming. I think it was this one: https://youtu.be/1-dUkyn_fZA It sounds like org mode does not store images inline, since you don't like the b…

>If you have to package images separately when sharing, then wouldn't inline images score a point for easier sharing? I guess that depends on who you're sharing with and how. If you're using git, you can just add them to your repo (only they won't clobber your diffs). If you're just publishing, you can export to HTML and put it somewhere online. >Agreed, and that is powerful, but this also goes to my point. Jupyter i…

Jupyter isn’t competing with emacs, it’s not an editor. It’s competing with the python shell. And it’s editing capabilities are way better than the python shell.

Adding git as a dependency to sharing is too much in general, that would prevent sharing.

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

#127

Post by jononor »

gaius wrote: post #66
PopePompous wrote: post #63

Earlier quoted context omitted.

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…

Reducing the barriers for doing reproduction studies will likely increase how often they happen.

Of just consider peer review. How often does a reviewer today actually review the code and data used in a study? As far as I know this is essentially never done. That would involve seeing the code, running it, maybe messing a bit with it.

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

#128

Post by carreau »

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.

Sorry, Fernando as well as all the contributors are included in the "we, the Jupyter team". I did not start to mention individuals otherwise the list would be really long. I would encourage people to look at (at minimum) the steering council on Jupyter.org for a list of key people in the project.

We are also striving to make contributing to Jupyter / open source recognized in Academia - for people like Fernando to get proper recognition, and future generations of scientists to have incentives to do this kind of work.

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

#129

Post by carreau »

nerdponx wrote: post #70
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…

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.

Fun fact, as far as the Jupyter team can tell, there are more full time Dev on Jupyter than CPython. Also pretty excited that bumpy recently got funding for 2 full time Dev that will work at UC BIDS!

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

#130

Post by ChrisRackauckas »

rexpress wrote: post #67
iguy wrote: 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.

There was a bug in Mathematica 10.0.3 that messed up saving parts to PDFs though. I wonder if he was on the release where this was broken:

https://mathematica.stackexchange.com/questions/68893/save-a...

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