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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

#21

Post by m_sahaf »

antt wrote: post #10
osrec wrote: post #8

Earlier quoted context omitted.

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…

> investment banker As someone who was a software engineer in a brokerage and had to deal with clients excel sheets: open/libre office not letting you do that is a feature. We would be given excel sheet that would depend on a specific version of Excel. We had sheets in the hundreds of megabytes. We had sheets that would take overnight to run. We had sheets with sheet dependencies. We had sheets that needed to be run…

I keep saying this to my friends: I dream of the day when people exchange SQLite files instead of XLS(X), and Excel, and the like, are just an interface to that database. This way you get data integrity (Excel randomly truncating digits or converting numbers to scientific notation is the bane of my existence), data present in raw form, and being interface/view layer agnostic.

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

#22

Post by hazz99 »

tincholio wrote: post #19
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…

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?

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

#23

Post by Vinnl »

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?

If you're really interested in this, you should contact Ivo Jimenez and Felix Z. Hoffmann. Although there's not much information available, under the heading of " Reproducible Computational Research – a case study " at [0], they tentatively explored such an idea at a hackathon in Cambridge in May.

[0] https://elifesciences.org/labs/bdd4c9aa/elife-innovation-spr...

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

#25

Post by sametmax »

mindcrime wrote: post #7
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.

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.

I use it almost exclusively.

And it crashes. It crashes and loose your work.

Regularly.

I love that such product exists. I donate to libre office.

But it's nowhere as reliable as msoffice. Any complex enought document will make it crash at some point.

It's not even reproductible. You can't pinpoint the action that made it crash. Sometime you do the same other and other and it's fine. Then it destroy work and crush your soul.

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

#26

Post by jk27277 »

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.

Try softmaker office

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

#28

Post by sghiassy »

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?

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

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

#29

Post by techphys_91 »

sghiassy wrote: post #28
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?

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.

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

#30

Post by dorfsmay »

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…

> it is painfully obvious that OO/LO cuts corners at certain places. For example, the mathematics of Calc is intentionally bugged

What about Gnumeric?

My understanding is that the dev team (mainly Jody Goldberg really) have focused on accuracy. The gnumeric.org site has links to studies related to its accuracy.

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