Microsoft’s purchase of GitHub leaves some scientists uneasy • Hacker News Board

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#31

Post by IanCal » Sat, Jun 16, 2018, 7:06 AM UTC

Fomite wrote: post #25

saagarjha wrote: post #16

This article seems to have a very focused interest on data in GitHub repositories, as opposed to source code. I get that the article is aimed at scientists, but I don’t see the problem here: if Microsoft takes down your dataset just move it somewhere else. You’re not tied down with pull requests or comments like code repositories are.

The problem is the stable of the pointer. From a paper of mine: "The code and simulation results are available online at https://github.com/mylabname/ project." That's in print . In another paper, I expressly cite a GitHub repository as the source of the data used in the analysis. Pointing to data in papers is the way most of the scientists I know use GitHub - because it's relatively stable, not tied to an institutio…

[disclaimer work for related company - Digital Science]

It's really worth getting those things into a system that will give you a doi and participate in an archive so that content should never be lost. Figshare is one, zenodo another (I think but can't find on a phone that the data is archived).

A doi, if versioned, can ensure people see the actual version you used. It can be pointed somewhere else if the provider goes down, and should be archived to ensure its not lost.

URLs are just not stable over time.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#32

Post by randomsearch » Sat, Jun 16, 2018, 7:06 AM UTC

geoalchimista wrote: post #30

To be honest, I don't think GitHub is to be blamed for how scientists use it. AFAIK there are data repositories more suitable for the purpose of sharing data sets and metadata, and out of the hands of big corporations (but may subject to big governments), e.g., Zenodo (funded by CERN) and DataONE (funded by NSF). Zenodo can even generate a DOI for your data set, which GitHub does not do. That being said, I think this…

“Why don’t scientists use modern tools like GitHub, instead of these crap bespoke ones? They shouldn’t waste their time duplicating effort.”

“Why are scientists using inappropriate tools? These are for commercial use only!”

In practice, GitHub works fine for collaborative code projects and sharing data over the next few years. If you’re looking to store large amounts of data over long periods, you’re right.

If GitHub don’t want to support science (they’re just a business) then they should stop giving free products to academia eh.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#33

Post by jeremy_wiebe » Sat, Jun 16, 2018, 7:07 AM UTC

freeone3000 wrote: post #20

gaius wrote: post #8

Earlier quoted context omitted.

the chances of them just scrapping the whole service are slim, and "GitHub disappears" seems equally as likely burning through VC cash as it does owned by Microsoft. Right, the people who should really be worried are VSTS users. And GitLab users funnily enough. They are VC backed and will have to exit too, and everyone’s looking at them now. The least worst thing that could happen is bought by Atlassian and folded in…

VSTS does a lot of stuff GitHub doesn't, and has had GitHub as a source control option for a while.

GitHub or just git? I thought just the latter.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#34

Post by kwhitefoot » Sat, Jun 16, 2018, 7:08 AM UTC

jarfil wrote: post #12

masonicb00m wrote: post #10

The cool thing about git is it doesn’t matter what happens to the platform. You can take your repo and push it somewhere else if you don’t like how Microsoft runs the show. Given how Microsoft took Github’s idea with Atom and ran with it to make VSCode, I wouldn’t be surprised if Github improves under Microsoft’s rule.

The problem lies in the comments and issue tracking, which are not stored in git. Sure, you can clone the repo, but you can only take the wiki with you, the rest would be lost.

Surely it ought to be possible to store all that stuff in git as well.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#35

Post by earenndil » Sat, Jun 16, 2018, 7:09 AM UTC

gaius wrote: post #8

Fomite wrote: post #2

"During the 2014–16 Ebola outbreak in West Africa, for example, researchers used the platform to share and cross-check daily patient counts." Pretty sure this is referring to the lab I used to work in. Honestly, I'm not particularly worried about the buyout - pretty sure the chances of them just scrapping the whole service are slim, and "GitHub disappears" seems equally as likely burning through VC cash as it does ow…

the chances of them just scrapping the whole service are slim, and "GitHub disappears" seems equally as likely burning through VC cash as it does owned by Microsoft. Right, the people who should really be worried are VSTS users. And GitLab users funnily enough. They are VC backed and will have to exit too, and everyone’s looking at them now. The least worst thing that could happen is bought by Atlassian and folded in…

IIRC they've said they intend to keep VSTS and github as separate products.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#36

Post by ulrikrasmussen » Sat, Jun 16, 2018, 7:12 AM UTC

Fomite wrote: post #25

saagarjha wrote: post #16

This article seems to have a very focused interest on data in GitHub repositories, as opposed to source code. I get that the article is aimed at scientists, but I don’t see the problem here: if Microsoft takes down your dataset just move it somewhere else. You’re not tied down with pull requests or comments like code repositories are.

The problem is the stable of the pointer. From a paper of mine: "The code and simulation results are available online at https://github.com/mylabname/ project." That's in print . In another paper, I expressly cite a GitHub repository as the source of the data used in the analysis. Pointing to data in papers is the way most of the scientists I know use GitHub - because it's relatively stable, not tied to an institutio…

Well, it still has a higher chance of being alive than other common alternatives. From my experience, any url put in a CS paper has a very high risk of being dead just a few years after publication. It seems that once the research grant has run out and the researchers have moved on, noone takes on the responsibility of ensuring that the web page is kept alive. Domains and hosting plans are not renewed; universities reorganize their departments and don't map the old URLs to the new ones; or policies change, and personal department hosted web pages for researchers are closed. The solution has to be some kind of independent library service for researchers, like arxiv for data/source code, which is guaranteed to be kept alive.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#37

Post by randomsearch » Sat, Jun 16, 2018, 7:12 AM UTC

Fomite wrote: post #25

saagarjha wrote: post #16

This article seems to have a very focused interest on data in GitHub repositories, as opposed to source code. I get that the article is aimed at scientists, but I don’t see the problem here: if Microsoft takes down your dataset just move it somewhere else. You’re not tied down with pull requests or comments like code repositories are.

The problem is the stable of the pointer. From a paper of mine: "The code and simulation results are available online at https://github.com/mylabname/ project." That's in print . In another paper, I expressly cite a GitHub repository as the source of the data used in the analysis. Pointing to data in papers is the way most of the scientists I know use GitHub - because it's relatively stable, not tied to an institutio…

In practice, the pointers are the authors.

In Computer Science, it’s a mess that works fine in practice. I go to GitHub - if it’s not there, then I google the authors or the name of the project. And I don’t know what I do if I don’t find any of them or their projects, because I’ve never encountered that scenario.

I’ve never seen a paper more than say 10 years old and thought “god I wish I had their code/data” because CS moves at a rapid speed. Important stuff is preserved because other people build on it. For example, it becomes the basis of an open source project.

Whilst from a rigorous and idealistic point of view, we want central long term data storage, in practice right now the real problem is that _many scientists do not make their data and code available in any form at all_ rather than worrying about pointers decaying.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#38

Post by lotia » Sat, Jun 16, 2018, 7:14 AM UTC

Seeing this published on Nature's website is quite thick with irony. They have profited greatly from locking up access to academic papers in their most prestigious journals.

The article includes the following tweet:

“Open Science is not compatible with one corporation owning the platform used to collaborate on code. I hope that expert coders in #openscience have a viable alternative to #github,” tweeted Tom Johnstone, a cognitive neuroscientist at the University of Reading, UK.

Github's current position is to be default open with a paid option for private. Nature's default position was to lock up journal articles and sell them for extortionate prices.

It's surprising to see them post an article noting that scientists feel MS will change that for the worse. They have been good participants in the open source community of late specially under Mr. Nadella's leadership.

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#39

Post by tandav » Sat, Jun 16, 2018, 7:14 AM UTC

masonicb00m wrote: post #10

The cool thing about git is it doesn’t matter what happens to the platform. You can take your repo and push it somewhere else if you don’t like how Microsoft runs the show. Given how Microsoft took Github’s idea with Atom and ran with it to make VSCode, I wouldn’t be surprised if Github improves under Microsoft’s rule.

So many repos don't use wiki. Just create docs/ folder and store .md there

Re: Microsoft’s purchase of GitHub leaves some scientists uneasy

#40

Post by gaius » Sat, Jun 16, 2018, 7:14 AM UTC

earenndil wrote: post #35

gaius wrote: post #8

Earlier quoted context omitted.

the chances of them just scrapping the whole service are slim, and "GitHub disappears" seems equally as likely burning through VC cash as it does owned by Microsoft. Right, the people who should really be worried are VSTS users. And GitLab users funnily enough. They are VC backed and will have to exit too, and everyone’s looking at them now. The least worst thing that could happen is bought by Atlassian and folded in…

IIRC they've said they intend to keep VSTS and github as separate products.

they intend to keep VSTS and github as separate product

Still, consider Codeplex, which isn’t around anymore.

I see the two merging over time, say in 5 years, and I expect the migration to be fairly painless, so I am not too worried personally, but I can see how some people might be.