Past, Present and Future of Open Science (Emergent session): Containers: Ticket to Valhalla or Ticket to the Inferno?

[jsheunis]

Containers: Ticket to Valhala or Ticket to the Inferno?

By David Kennedy, University of Massachusetts Medical School

• Theme: Past, Present and Future of Open Science
• Format: Emergent session

Abstract

The containerization of neuroimaging analysis workflows has quickly become a hot topic in the OSR and beyond. But with great power comes great responsibility. Containers sometimes get presented as the 'end all and be all' by some and as a 'dangerous bandaid for masking bad software development practices' by others. What's the poor researcher to do? In this session we hope to have a pleasant discussion of the pros and cons, useful application areas, and practical logistics about using containers in the 'real world'.
We propose to present this as a round table with input from a number of perspectives, then followed by a dialog and public discussion aimed at determining where the community stands regarding 'best practices' and use of containers. The round table may include (subject to confirmation and further discussion): Jo Etzel, Pierre Bellec, Peer Herholz, Satra Ghosh, Agah Karakuzu.

Useful Links

https://github.com/ReproNim/neurodocker
https://ww5.aievolution.com/hbm1901/index.cfm?do=abs.viewAbs&abs=4639

Tagging @dnkennedy

[PeerHerholz]

tagging @satra, @dnkennedy, @jaetzel and @pbellec as interested folks based on the Mattermost thread. Did I miss anyone/who else should be tagged?

[gllmflndn]

Great! Don't forget @stebo85

[PeerHerholz]

Thx @gllmflndn, was also thinking about @stebo85, but wasn't sure if he could make it given the time zones! @stebo85 is a there a time that would work for you?
Also saw that I forgot @agahkarakuzu, sorry.

[lunebellec]

LGTM. I think Gael Varoquaux has pretty strong opinions about 'dangerous bandaid for masking bad software development practices' (could not locate the link, but I think he wrote a blog post about that a while back).

It would also be great to have someone speak about reproducibility and containers. Maybe Valerie Hayot?

I am happy to be dropped from the discussion, as I don't think I have expertise not covered by others. I guess I could play the role of devil's advocate, as I am not sold on the utility of containers as a software distribution tool.

[PeerHerholz]

tagging @ValHayot, thx @pbellec.

[gllmflndn]

Please stay @pbellec, we need a diversity of opinions!

Searching for Gael's blog post, I found this:
http://gael-varoquaux.info/programming/of-software-and-science-reproducible-science-what-why-and-how.html
http://ivory.idyll.org/blog/2014-containers.html

[PeerHerholz]

tagging @GaelVaroquaux to check if he would be interested and has bandwidth to stop by.

[GaelVaroquaux]

Happy to complain :).

When exactly do you need me?

[PeerHerholz]

thx @GaelVaroquaux, the rock of complains, hehe! Also tagging @hcp4715 who did a lot of work to introduce containers in his lab/institute and certainly has important and interesting points to add.

[hcp4715]

@PeerHerholz, FYI, yesterday we have an excellent master student in China wrote a Chinese tutorial that covered the whole process from installing docker, to using heudiconv, and running fmriprep, in both Linux and Windows (you can imagine the frustrations he had experienced ;)). We put is on OSF: https://osf.io/naxgd/

[ValHayot]

Hey, thanks for the tag. While I do have opinions, I'm no expert on the matter. I'll tag @gkiar and @ali4006 who have done extensive work on this.

I'll try to listen in though :)

[PeerHerholz]

Thx @hcp4715, cool! Following up on our conversation in Mattermost: we need a diverse set of experience levels, use cases and backgrounds in order to create a fruitful discussion. So far I think the following have been mentioned (thx @emdupre):

• tool developers that use containerization
• tool developers for containerization
• software consumers in small projects
• software consumers at scale
• educators that taught containerization

Please discuss and add further groups!