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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

#31

Post by sghiassy »

techphys_91 wrote: post #29
sghiassy wrote: post #28

Earlier quoted context omitted.

Also the most widely used language 6 years in a row: https://insights.stackoverflow.com/survey/2018/#most-popular...

That by itself doesn't count for much in this context. Web based technologies tend to move quickly while scientists are almost all using math libraries that were written in the 60/ 70's. To scientists these things are just tools and they prefer stability, reproducibility and minimal dependencies over using what's popular.

I doubt there’s much that can be said her to sway anyone’s mind.

Either way, wish the project luck! Reproducible scientific studies is paramount.

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

#32

Post by gkya »

sghiassy wrote: post #31
techphys_91 wrote: post #29

Earlier quoted context omitted.

That by itself doesn't count for much in this context. Web based technologies tend to move quickly while scientists are almost all using math libraries that were written in the 60/ 70's. To scientists these things are just tools and they prefer stability, reproducibility and minimal dependencies over using what's popular.

I doubt there’s much that can be said her to sway anyone’s mind. Either way, wish the project luck! Reproducible scientific studies is paramount.

Not really. Reproducible research depends on reproducible execution, which depends on a reproducible environment, which depends on a reproducible set of libraries and frameworks. I don't think Node is apt for that. The community values new over stable, and cool over technically superior. That might have its value, but I do not believe those are valuable traits for a project of this sorts.

That it's popular means nothing. Windows is the most popular operating system, pop is the most popular genre of music, oil is the most popular fuel, since decades. This doesn't invalidate their utility or our appreciation of them, but it does not mean they're good for everything.

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

#34

Post by basiliskparty »

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.

Not disagreeing with you, as everyone has different workflows etc. but my experience is really different. I've found LibreOffice entirely suitable for heavy duty work, completely fine.

Microsoft products crash inexplicably on our systems too, and in fact, we have much weirder problems with corrupted instances and things than we've ever had when using LibreOffice. I also have serious problems with the Office UI, basically that the ribbon UI as it's implemented is inconsistent and incoherent, which is frustrating as hell. If you're going to have a ribbon/tab UI, make it consistent throughout, and don't have special exceptions for some functions.

Having said that, I do think LibreOffice loses to Microsoft's edge in some areas of polish, like in implementing equations, and in drawing figures. Some of the UI with the drawing actions are much more intuitive in Office.

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

#35

Post by basiliskparty »

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?

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

#36

Post by tincholio »

hazz99 wrote: post #22
tincholio wrote: post #19

Earlier quoted context omitted.

It's a bit more complex than that, as it's not just having access to the software, but to the whole environment. The move towards reproducible builds and configurations (Nix and the like) is a good thing for this, as well.

I've come across this problem before (as a third party - I don't do research) and I've considered writing software to help solve it. Maybe something like a Jupyter notebook with an attached mini-filesystem that can be easily shared with colleagues? What do you think would be a required to solve this?

It depends a lot on the field. In my own work (I'm out of academia now, but it still applies), there's often very complex network setups involved, so a Jupyter notebook won't quite cut it. Many things in this particular domain can be nowadays solved with SDN, but it is still a complicated issue. I'm sure people from other fields have analogous problems, too. And this is in CS, I suspect that anything which implies more "physical" setup is orders of magnitude more complex.

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

#38

Post by hjek »

osrec wrote: post #8
mindcrime wrote: post #7

Earlier quoted context omitted.

I'm not sure why, but open/libreoffice is almost unusable for heavy duty office work. What do you define as "heavy duty office work"? What would make OpenOffice more suitable to you needs? Asking as an AOO contributor. I'm genuinely curious to know what you think the project is lacking or how it needs to be improved.

Firstly, I would like to thank you for your work. Open office has served me very well during my school and university days. Since joining the world of work, I've struggled with the following: - Random crashes every couple of hours when files become large. Especially in Impress and Calc. - I do a lot of diagrams in OODraw. Sometimes I'll reopen the file to find arrows and connectors have moved. - The interface could b…

For the last few years most of the work has been happing in the LibreOffice fork. If OO crashes on you, try LO.

https://lwn.net/Articles/699755/

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

#39

Post by gnufx »

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 experiments and large-scale calculations with which I'm most familiar the way people are suggesting, and software engineering can't address bad science or lack of information. Revision control and "notebook" interfaces seem to have become the equivalent of waving XML metadata at any problem from the days when e-science was preventing useful work and research. Experience from a non-trivial research record and some decades doing and supporting research computing will be ignored, though.

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

#40

Post by gnufx »

writepub wrote: post #37

How's stencila supposed to produce reproducible research? No one's fudging the formulae, they're fudging data. And stencila will digest whatever data you give it, real or fake

Hear, hear! Even if they're not fudging them as such, they may have cocked up the measurements. You figure that out from hard experience in the field (or relevant experience from another, which is often very helpful), not with some trendy piece of software.
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