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Stencila: An open source office suite for reproducible research

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Re: Stencila: An open source office suite for reproducible research

#41

Post by nokome »

mockingbirdy wrote: post #20

If any contributor sees this: The "Learn" link in the footer points to a 404 Github page. Is this usable for daily usage? And can we output PDF and use LaTeX for publications?

Hi, Stencila dev here. In my opinion, Stencila is not ready for daily usage. But we are looking for beta testers who are willing to put up with bugs and crashes and help us shape the framework. We have converters, based on Pandoc, which are able to convert to both PDF and Latex - although they are also in preliminary development.

Re: Stencila: An open source office suite for reproducible research

#42

Post by nokome »

gkya wrote: post #27

So this is a reproducible research application suite built on Node.JS, the epitome of non-reproducibility and characterised by fast pace, little care for compatibility, and an ecosystem of volatile libraries?

Hi, Stencila dev here, thanks for the feedback. There are several modular components that make up Stencila. The user interface modules are indeed built using Javascript, and Node.js is used in a number of places including the desktop and CLI apps and format converters. But for code execution, Stencila does not rely on Node, and users can use R, or Python or SQL.

> Reproducible research depends on reproducible execution, which depends on a reproducible environment, which depends on a reproducible set of libraries and frameworks.

Completely agree. We are trying to make it easy for people to use reproducible libraries and environments. To this end, we are developing Nix environments (a highly reproducible way of defining computing environments) which include Stencila "execution contexts" for R, Python etc with standard libraries included. These environments can be connected to the user interface. See https://github.com/stencila/images/ for more details.

Re: Stencila: An open source office suite for reproducible research

#43

Post by nokome »

jsilence wrote: post #18

Interresting! Does Stencilla offer any kind of author collaboration? Publication are usually not one person efforts and research teams oftentimes are not working in the same location. In my experience the GDocs or Word comments and revise mode are heavily used in collaborations.

Thanks for the feedback. Comments and "track changes" are a commonly requested feature, important for collaboration, and certainly something we want to implement!

Re: Stencila: An open source office suite for reproducible research

#44

Post by nokome »

basiliskparty wrote: post #35
jsilence wrote: post #18

Interresting! Does Stencilla offer any kind of author collaboration? Publication are usually not one person efforts and research teams oftentimes are not working in the same location. In my experience the GDocs or Word comments and revise mode are heavily used in collaborations.

I was wondering that too. It seems like there might be collaborative editing, given dat project involvement?

Yes, we'd love to have real-time collaboration, preferably in a decentralised way using Dat!

Re: Stencila: An open source office suite for reproducible research

#45

Post by nokome »

sheetjs wrote: post #12
osrec wrote: post #5

This looks interesting. I'm actually rather surprised at the lack of quality in most open source 'office' alternatives. I'm not sure why, but open/libreoffice is almost unusable for heavy duty office work. Microsoft products are the clear winners if you require productivity and stability. I really hope that changes soon, because I feel it's a major factor that holds back widespread Linux adoption.

There's a ton of mindnumbing testing and grinding work that honestly no one really wants to do, involving bit-level accuracy in many cases. We ( https://sheetjs.com/ ) are attacking the file compatibility problem (our major open source project is https://github.com/sheetjs/js-xlsx , used in stencila's spreadsheet converters) and it is painfully obvious that OO/LO cuts corners at certain places. For example, the mathe…

Just a quick word of thanks for SheetJs from a Stencila dev! All the "mindnumbing testing and grinding work that honestly no one really wants to do" is obvious and much appreciated. Your efforts are so important for the ensuring interoperability but are often not recognised because they are "in the backend".

Re: Stencila: An open source office suite for reproducible research

#46

Post by gkya »

nokome wrote: post #42
gkya wrote: post #27

So this is a reproducible research application suite built on Node.JS, the epitome of non-reproducibility and characterised by fast pace, little care for compatibility, and an ecosystem of volatile libraries?

Hi, Stencila dev here, thanks for the feedback. There are several modular components that make up Stencila. The user interface modules are indeed built using Javascript, and Node.js is used in a number of places including the desktop and CLI apps and format converters. But for code execution, Stencila does not rely on Node, and users can use R, or Python or SQL. > Reproducible research depends on reproducible executi…

Thanks for the explanations!

Re: Stencila: An open source office suite for reproducible research

#48

Post by a_136_chiffa »

gnufx wrote: post #39
buchanae wrote: post #17

> The calls for research to be transparent and reproducible have never been louder. But today's tools for reproducible research can be intimidating - especially if you're not a coder. As someone (a software engineer) who has been trying (struggling) to reproduce biology research lately, I say amen. Hallelujah. But. It's time to accept coding as a core skill. Science has more to learn from software engineering than it…

I'm baffled how "coding" equates to software engineering. If anything, scientists probably need to listen less to current Research Software Engineering dogma, and RSE types need to learn more about science. (Few will even take measurement seriously in my experience.) The "reproducibility" mantra is at odds with a lot of real world science and serious computing. You don't/can't in general reproduce the sort of physics…

The issue is not to repeat the experiments, but rather to avoid putting the logs in the wheels of people who want to re-analyze your existing data (including yourself a couple of years later) and avoid losing thousands of working hours doing forensic data analysis to point out shitty science. Keith's Baggerly 2010 talk on the hoops he had to jump through to get to Anil Potti (https://en.wikipedia.org/wiki/Anil_Potti) is a great demo of the application case: https://youtu.be/7gYIs7uYbMo.

And as for "doing real science" vs. trying to make it more reproducible, there is an excellent analogy with "doing real programming" (aka adding features) vs. refactoring and architectural adjustments. Telling that you consider the second as a waste of time tells more about yourself than about the subject.

Re: Stencila: An open source office suite for reproducible research

#49

Post by erAck »

sheetjs wrote: post #12
osrec wrote: post #5

This looks interesting. I'm actually rather surprised at the lack of quality in most open source 'office' alternatives. I'm not sure why, but open/libreoffice is almost unusable for heavy duty office work. Microsoft products are the clear winners if you require productivity and stability. I really hope that changes soon, because I feel it's a major factor that holds back widespread Linux adoption.

There's a ton of mindnumbing testing and grinding work that honestly no one really wants to do, involving bit-level accuracy in many cases. We ( https://sheetjs.com/ ) are attacking the file compatibility problem (our major open source project is https://github.com/sheetjs/js-xlsx , used in stencila's spreadsheet converters) and it is painfully obvious that OO/LO cuts corners at certain places. For example, the mathe…

As you referenced that bug and there also gave an example involving fractions and =0.1+0.2 you would certainly also agree that the binary floating point representation of =0.1+0.2-0.3 is not 0.0, still Excel displays 0 as result (and so does Calc) instead of 5.551115123125783E-17 because users expect that.

Your bit-level accuracy approach isn't as simple when it comes to user experience and Excel compatibility.

Re: Stencila: An open source office suite for reproducible research

#50

Post by erAck »

erAck wrote: post #49
sheetjs wrote: post #12

Earlier quoted context omitted.

There's a ton of mindnumbing testing and grinding work that honestly no one really wants to do, involving bit-level accuracy in many cases. We ( https://sheetjs.com/ ) are attacking the file compatibility problem (our major open source project is https://github.com/sheetjs/js-xlsx , used in stencila's spreadsheet converters) and it is painfully obvious that OO/LO cuts corners at certain places. For example, the mathe…

As you referenced that bug and there also gave an example involving fractions and =0.1+0.2 you would certainly also agree that the binary floating point representation of =0.1+0.2-0.3 is not 0.0, still Excel displays 0 as result (and so does Calc) instead of 5.551115123125783E-17 because users expect that. Your bit-level accuracy approach isn't as simple when it comes to user experience and Excel compatibility.

Regarding your fraction example there:

=RAWSUBTRACT(0.1,-0.2,1/3) => -0.033333333333333

=RAWSUBTRACT(0.1,-0.2,2/7) => 0.014285714285714

So which one is closer to 0.3?

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