Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread W. Trevor King
On Tue, Mar 01, 2016 at 08:53:35AM -0500, Pat Schloss wrote: > … one of the strengths that I feel formal version control wins with > vs. dropbox is that I can rm -rf my_project and do a pull from > github and get my project back. I think the main strength of distributed version control over

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Maria McKinley
My way of convincing my lab to use version control was showing them how if we introduced a bug into the software running our experiment, I could have the code back to the way it was the previous day in less than 30 seconds. That plus being able to upgrade all of the experimental rigs to new

Re: [Discuss] Versatile PhD

2016-03-01 Thread Martin Bähr
Excerpts from Davide Del Vento's message of 2016-02-28 20:45:09 +0100: > For the rest, I agree with the whole group that Martin Bahr's views > are pretty chauvinist and out of date. i asked davide about this and we realized that my quote of uncle bob was misunderstood. first of all, what davide

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Davide Del Vento
> Students (both those that have worked with servers/clusters before > and those that haven't) find this workflow very compelling (need a > faster computer? one with more memory? you can use one in the > cloud for free! here's how to do that easily...), Easily if they remember how to use git

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Bennet Fauber
Greg, Quite a bit of the discussion since I started this reply seems to hinge on git being useful because of github and cloudiness. I'm going to go back to your original two questions and ignore the cloud, if I may? For your question 1, I might comment that LD50 isn't usually given all at once,

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread C. Titus Brown
On Tue, Mar 01, 2016 at 08:02:03AM -0700, naup...@gmail.com wrote: > My sense is that the strength of many of the tools SWC teaches comes when > analyses are scaled up in complexity or size; +inf. I don't know if it's possible, but I would love to see this argument laid out for novices in a

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread naupaka
Hi all - Following up on one of Pat's points, I think one of the biggest selling points when teaching git (or other version control) to novices is how much easier it makes working on remote machines. I've taught SWC workshops with iPlant/CyVerse several times now, and the capstone exercise is

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Pat Schloss
As I’m in the midst of teaching git, this has been a really important conversation for me since many of my learners are wondering about how to put word/excel/etc under version control and why something like dropbox wouldn’t work. While they think git is interesting, they also appear somewhat

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Davide Del Vento
> 2. What should we say to someone like Arjun? It's clear from his > post that he knows the arguments in favor of version control, and > has actually tried it. It's also clear that he cares about doing things > well - what can we do to convince someone like that? > > It's always too much trouble

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Greg Wilson
Re-reading Arjun Raj's post (http://rajlaboratory.blogspot.ca/2016/02/from-reproducibility-to-over.html), I've got a couple of thoughts. First, I think some of the disparaging comments on Twitter and elsewhere were unhelpful: they're unlikely to get the author to change his mind, and it

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Erik Bray
On Mon, Feb 29, 2016 at 10:45 PM, Byron Smith wrote: > Not really on topic here, but maybe we should be teaching learners `git > reflog show` [1]. Everyone messes git up sometimes; Checking the reflog is > often the best fix when that happens. > > On the other hand, the

Re: [Discuss] RajLab: From reproducibility to over-reproducibility

2016-03-01 Thread Erik Bray
On Mon, Feb 29, 2016 at 8:06 PM, Davide Del Vento wrote: >> if you’re like me, you will screw up at some point, leading to some problem, >> potentially catastrophic, that you will spend hours trying to figure out. >> I’m clearly not alone... “Abort: remote heads