Jupyter, Mathematica, and the Future of the Research Paper • Hacker News Board

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

#21

Post by bloaf » Sun, Apr 15, 2018, 5:01 AM UTC

ChrisRackauckas wrote: post #19

mlevental wrote: post #10

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…

Re: Speed

Mathematica is undergoing a compiler re-vamp, which may change that.

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

#22

Post by acidburnNSA » Sun, Apr 15, 2018, 5:01 AM UTC

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…

Fair points. Just to clarify I think the author was referring to Vandals [1] in the original sense rather than merely poking fun.

[1] https://en.wikipedia.org/wiki/Vandals

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

#23

Post by FractalLP » Sun, Apr 15, 2018, 5:02 AM UTC

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 equivalent to "there is a function for that".

Graph Theory works flawlessly in Mathematica. In Python, there is a module to Graphviz. Let me know if Python has something new though. There are a lot of other examples. Mathematica's Import[] function can read over 150 different file types including: CSV,.XLS, genetic encoding files, optimization files....whatever. It is usually far easier and more consistent than finding a corresponding Python library and struggling with the install and minimal documentation. Let me be clear that Python is awesome and rocks and i think Jupyter is moving it in the right direction. I just feel like many dismiss Mathematica as something that does Calculus homework rather than what it is today which is a massive 20 million LOC conglomeration of C & Java & Wolfram language that does everything from Statistics, Machine Learning, Visualization, BlockChain, 3D printing, NodeGraphs, data sets and analysis...etc in a single consistent package. It is expensive and proprietary and certainly has its own faults, but a lot of that cash is funneled back into a great product.

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

#24

Post by williamstein » Sun, Apr 15, 2018, 5:07 AM UTC

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 viable open source alternative to the core Mathematica computer algebra system (and also to Magma, etc.), whereas the goal of CoCalc is to make all technical open source software very, very easily accessible, mainly to students.

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

#25

Post by williamstein » Sun, Apr 15, 2018, 5:10 AM UTC

forapurpose wrote: post #7

> Python libraries let me replicate everything I wanted to do with Mathematica: Matplotlib for graphics, SymPy for symbolic math, NumPy and SciPy for numerical calculations Are the Python libraries precise enough for professional mathematicians? And do they deal with mathematical 'edge cases', a variety of inputs (formats, notations, etc.), etc.? On one hand, I could say 'the author uses them therefore they must be s…

SageMath (which I started in 2004) is in fact a Python library targeted at professional mathematicians (mainly research in pure math), and is much stronger than Mathematica in many areas, including number theory, algebraic combinatorics and algebraic dynamics. It is weaker than Mathematica in symbolic calculus.

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

#26

Post by mlevental » Sun, Apr 15, 2018, 5:13 AM UTC

ChrisRackauckas wrote: post #19

mlevental wrote: post #10

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…

>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...

yup. for quick and dirty type setting i preferred it to latex

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

#27

Post by askvictor » Sun, Apr 15, 2018, 5:34 AM UTC

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 needs to use open source tools.

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

#28

Post by askvictor » Sun, Apr 15, 2018, 5:37 AM UTC

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)

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

#29

Post by applecrazy » Sun, Apr 15, 2018, 5:39 AM UTC

smortaz wrote: post #16

carreau wrote: post #11

Earlier quoted context omitted.

Thanks for your feedback, Mathematica has indeed millions of $ to provide more features and advertise them, and Jupyter have only a few full time devs that probably do not advertise enough its features: 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-…

MyBinder is great. As well as cocalc and sagemath. There's also https://notebooks.azure.com which is a free hosting of Jupyter notebooks. You get a linux/docker container w a Terminal, Anaconda, etc. Check out jakevp's book for example: https://notebooks.azure.com/jakevdp/libraries/PythonDataScie... Clone to run. Also try Jupyter Lab (experimental) - closer to an IDE than plain notebooks. right click on a Library (re…

There’s also Google Colaboratory

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

#30

Post by askvictor » Sun, Apr 15, 2018, 5:40 AM UTC

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.