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

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

#21

Post by Fomite » Sat, Jun 16, 2018, 6:33 AM UTC

johnchristopher wrote: post #9

> "[..] researchers used the platform to share and cross-check daily patient counts." No concerns about private datasets in the open on Github ? I get they like the workflow but they traded ethics for convenience there. Medical ethics.

These were publicly reported data sets of case counts. You can find them on various Ministry of Health websites.

I know because I worked in the lab that maintained one of them. The biggest issue was that one country reported their data in non-machine readable form on Facebook. Maintaining that was extremely time intensive.

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

#22

Post by Fomite » Sat, Jun 16, 2018, 6:35 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.

To my mind, the actual problem is neither one of those things, but if Github is wrapped up into some new project. Many of the citations for Github aren't for software, but as a stable, open store for data.

Which means if that URL changes, that link - in a physical paper - goes stale.

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

#23

Post by gpantazes » Sat, Jun 16, 2018, 6:35 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.

So what I'm hearing is the solution to this migration problem is to also store the entire issue tracker as a git repo alongside the real repo and wiki repo? Git repos for all the things! (Seriously, I think this solution would fit right in along with the way Wikis are handled)

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

#24

Post by Fomite » Sat, Jun 16, 2018, 6:37 AM UTC

craftyguy wrote: post #3

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…

For the current regime, mmaybe. But don't underestimate next regime's ability to flip tables.

I mean yeah, but that's always true. But until my next grant wants to pay for someone to deal with self-hosting, it's a risk I'll take.

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

#25

Post by Fomite » Sat, Jun 16, 2018, 6:40 AM UTC

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 institutional account, and relatively pain free.

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

#26

Post by Cyphase » Sat, Jun 16, 2018, 6:43 AM UTC

Fomite wrote: post #22

jarfil wrote: post #12

Earlier quoted context omitted.

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.

To my mind, the actual problem is neither one of those things, but if Github is wrapped up into some new project. Many of the citations for Github aren't for software, but as a stable, open store for data. Which means if that URL changes, that link - in a physical paper - goes stale.

Even if it does get merged or renamed, I don't see why Microsoft wouldn't forward the URLs.

Link rot is a real issue in general though, I don't mean to minimize that.

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

#27

Post by Fomite » Sat, Jun 16, 2018, 6:44 AM UTC

Cyphase wrote: post #26

Fomite wrote: post #22

Earlier quoted context omitted.

To my mind, the actual problem is neither one of those things, but if Github is wrapped up into some new project. Many of the citations for Github aren't for software, but as a stable, open store for data. Which means if that URL changes, that link - in a physical paper - goes stale.

Even if it does get merged or renamed, I don't see why Microsoft wouldn't forward the URLs. Link rot is a real issue in general though, I don't mean to minimize that.

I agree - which is why I haven't moved my lab's accounts.

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

#28

Post by mtgx » Sat, Jun 16, 2018, 6:47 AM UTC

ToFab123 wrote: post #13

"Open Science is not compatible with one corporation owning the platform used to collaborate on code" That was already the case before Microsoft purchased GitHub. So why did they start to use it in the first place, if they had this concern?

Maybe what he meant was one large corporation.

It's usually the large players that start taking down accounts at will and have bogus takedown rules, because they are the largest and don't care about any one account.

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

#29

Post by wpdev_63 » Sat, Jun 16, 2018, 6:49 AM UTC

ughh... just roll with your own git server.

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

#30

Post by geoalchimista » Sat, Jun 16, 2018, 7:03 AM UTC

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 Nature report adds nothing new to the narrative. Sure, open science is great, but who's gonna pay for it? Neither GitHub nor Microsoft is a charity. Since most of the research mentioned in this article are funded by government, they should go to the data repositories that are designed to store data derived from publicly funded research. GitHub just wasn't designed for that purpose.