GitHub:)

[oryoruk]

GitHub can help with:

• transparency
  • e.g. making scripts, codes public in a public github repo.
• reproducibility
  • e.g. having the commit history can others to use the exact version of a program in reproducing an analysis.

It addresses some of the issues with transparency and reproducibility, but not all so it's not sufficient.

[gwaybio]

Agreed! 👍 Paired with zenodo, it makes a powerful and citable versioned resource.

Although I have heard talks that Github is becoming too much of a monopoly and that if it ever went under for an extended period of time or was terminated for whatever reason, all benefits are obviously lost.

[oryoruk]

wow, zenodo is so cool. thank you Greg.

if it ever went under for an extended period of time or was terminated for whatever reason, all benefits are obviously lost.

with this user base, and underlying git's open nature, I doubt that. as long as you have your repo you can host it somewhere else. if they go down, I suspect bitbucket, others will fill in the void.

having said that with other tools on top, GitHub is more than its core functionality now. and that will take a little longer to develop for sure.

[gwaybio]

with this user base, and underlying git's open nature, I doubt that.

Yeah, me too, I hope its here to stay!

I think a much more likely scenario where github fails alone is when a github repo associated with a manuscript is deleted, updated, moved, or altered in any way that separates it from the paper submission. Sure a user can roll back commits to the submission date, but not in all situations...

[oryoruk]

Fair point. How can we make a persistent snapshot of a repo? :thinking: I love @greenelab's GitHub enthusiasm! 💯

[gwaybio]

We use github releases tied to a zenodo DOI. This may have some similar limitations though.

There are probably other solutions too!

[bemert]

First time using GitHub with this assignment. Seems pretty user friendly, but haven't yet tried using/commiting to more extensive scripts. Agree that it supports transparency, reproducibility, and collaboration. As mentioned by Greg and Onur above, having a permanent copy of one's work is important for research and may not be provided by Github.

[sklasfeld]

I have found github useful for both collaborations as well as doing my own personal projects. I like the history feature because I tend to change parts of scripts that I sometimes need to have not changed. Looking through the history, it is easy to fix mistakes using Github. However, I am still trying to learn the difference between branches and forks. Like most of the tools listed, there is a learning curve to getting the commands on the command line correct. For example, the difference between a commit and push is subtle.

[zz327]

Github is an awesome tool for colaberation and managing your own script. It could even generate website. However, I feel like for new user, the learning curve is quite steep. You have to keep practice to get use to it.