Hi Jan, I have the same concerns regarding many of the "tool heavy" solutions to reproducibility out there. Here's an essay I wrote recently proposing a solution that requires no special tooling: http://journals.ametsoc.org/doi/abs/10.1175/BAMS-D-15-00010.1
and here's the accompanying SWC lesson: http://damienirving.github.io/capstone-oceanography/ (I should say that SWC doesn't teach Docker or anything like that - the shell, command line programs and automation with Make lessons basically teach people everything they need to know to be reproducible. I basically wrote the capstone and essay just to make that more explicit, because sometimes I'm not sure that SWC participants realise that they've learned everything they need). Cheers, Damien <https://github.com/DamienIrving/CV/blob/master/CV.md> On Thu, Jan 14, 2016 at 6:06 AM, Jan Kim <[email protected]> wrote: > Dear All, > > I'm preparing a talk centred on reproducible computing, and as this is > a topic relevant and valued by SWC I'd like to ask your opinion and > comments about this. > > One approach I take is checking to which extent my work from 10 - 20 > years ago is reproducible today, and (perhaps not surprisingly) I found > that having used make, scripts and (relatively) well defined text > formats turns out to be higly beneficial in this regard. > > This has led me to wonder about some of the tools that currently seem > to be popular, including on this list, but to me appear unnecessarily > fat / overloaded and as such to have an uncertain perspective for long > term reproducibility: > > * "notebook" systems, and iPython / jupyter in particular: > - Will the JSON format for saving notebooks be readable / > executable in the long term? > - Are these even reproducible in a rigorous sense, considering > that results can vary depending on the order of executing cells? > > * Virtual machines and the recent lightweight "containerising" > systems (Docker, Conda): They're undoubtedly a blessing for > reproducibility but > - what are the long term perspectives of executing their images > / environments etc.? > - to which extent is their dependence on backing companies a > reason for concern? > > I hope that comments on these are relevant / interesting to the SWC > community, in addition to providing me with insights / inspiration, > and that therefore posting this here is ok. > > If you have comments on reproducible scientific computing in general, > I'm interested as well -- please respond by mailing list or personal > reply. > > Best regards & thanks in advance, Jan > -- > +- Jan T. Kim -------------------------------------------------------+ > | email: [email protected] | > | WWW: http://www.jtkim.dreamhosters.com/ | > *-----=< hierarchical systems are for files, not for humans >=-----* > > _______________________________________________ > Discuss mailing list > [email protected] > > http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org >
_______________________________________________ Discuss mailing list [email protected] http://lists.software-carpentry.org/mailman/listinfo/discuss_lists.software-carpentry.org
