A bit of a different domain but I wrote a tutorial for reproducible research in bioinformatics using conda package management, snakemake for workflow management and containerization using Singularity here: http://reproducible.sschmeier.com/
Cheers Sebastian Schmeier ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~ Dr. Sebastian Schmeier Research Group Leader Senior Lecturer in Bioinformatics/Genomics Institute of Natural and Mathematical Sciences Massey University Auckland [email protected] | https://sschmeier.com ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~ On Sat, 4 Aug 2018, 06:41 C. Titus Brown, <[email protected]> wrote: > Hi Sumana, > > I’m a big fan of mybinder.org, and the software stack it’s based on > (BinderHub and in particular repo2docker). > > repo2docker takes a repo with a rather standard & flexible “configuration > spec” and builds a Docker image out of it. > > mybinder.org, which is a free service running software called BinderHub, > stage manages the process of getting a GitHub repo name, building the > docker image, and then launching one or more containers of that image that > run either Jupyter or RStudio (or potentially any other Web site). > > repo2docker config info: > https://repo2docker.readthedocs.io/en/latest/config_files.html > > mybinder.org: https://mybinder.org/ > > binderhub: https://github.com/jupyterhub/binderhub > > There’s a collection of binder examples here, > > https://github.com/binder-examples > > and I would suggest taking a look at either > https://github.com/binder-examples/jupyterlab or > https://github.com/binder-examples/r - just go click the little “launch > binder” button on the README! > > All open source etc etc of course. > > best, > —titus > > > On Aug 1, 2018, at 9:39 PM, Sumana Harihareswara <[email protected]> > wrote: > > > > Friends and neighbors: what platforms for reproducible science > (including scientific computing) do you recommend? As in, "in order for you > to verify my results, you can go to this webpage/repository/etc. and > download the data I used and the code I wrote, and run the same > models/experiments to verify and reproduce my findings"? And is there an > existing platform and site that economists in particular gravitate toward, > and does it make a difference if the language in question is Python? > > > > I'm helping a client who wants to avoid reinventing the wheel. I include > a note about them & their current approach at the bottom of this email. > > > > There seem to be many different software projects and archives I should > explore, such as: > > > > * LabTrove > > http://www.labtrove.org/aboutus/ (example: > http://malaria.ourexperiment.org/ > > ) > > * Dryad > > https://datadryad.org/ > > > > * Open Science Framework > > https://osf.io/ > > > > * figshare > > https://figshare.com/ > > > > * RunMyCode > > http://www.runmycode.org/ > > > > * DAT > > https://datproject.org/ > > > > * finding a particular existing Dataverse or VisTrails instance? > > https://dataverse.org/ https://nyu.reproduciblescience.org/vistrails/ > > > > * ScienceFair > > http://sciencefair-app.com/ > > maybe? > > * Stencila > > https://stenci.la/ > > maybe? > > * use GitHub plus Jupyter notebooks or something like ReproZip > > https://www.reprozip.org/ > > > > > > > > Sorry if I'm lumping together things that are quite different from each > other! I'm at a bit of a loss here and may have missed a foundational > explanation/directory. > > > > My client's currently got a standalone GitHub repository: > > https://github.com/econ-ark/REMARK > > . I'll excerpt from their README to explain: > > > > > > > >> This is the resting place for self-contained and complete projects > written using [our tools]. > >> > >> Each of these resides in its own subdirectory in the REMARKs directory > >> > >> Types of content include (see below for elaboration): > >> > >> Explorations > >> Use the Econ-ARK/HARK toolkit to demonstrate some set of > modeling ideas > >> Replications > >> Attempts to replicate the results of published papers written > using other tools > >> Reproductions > >> Code that reproduces the results of some paper that was > originally written using the toolkit > >> > >> > > ... > > > > > >> Code archives should contain: > >> > >> All information required to get the replication code to run > >> An indication of how long that takes on some particular machine > >> > >> Jupyter notebook(s) should: > >> > >> Explain their own content ("This notebook uses the associated > replication archive to demonstrate three central results from the paper of > [original author]: The consumption function and the distribution of wealth") > >> Be usable for someone wanting to explore the replication > interactively (so, no cell should take more than a minute or two to execute > on a laptop) > >> > >> > > > > Much thanks. I would be happy to hear, for instance, "use this" or "it > depends very heavily on your needs, but DON'T use these because they're > vaporware/super-buggy". > > > > > > > > -- > > Sumana Harihareswara > > Changeset Consulting > > > > https://changeset.nyc > > > > > > P.S. Tried to send this earlier and it didn't seem to post, so, sorry if > this double-posts. > > The Carpentries / discuss / see discussions + participants + delivery > options Permalink > > ------------------------------------------ > The Carpentries: discuss > Permalink: > https://carpentries.topicbox.com/groups/discuss/T45d1f9e935d7181b-M1da834a8946c3647d96481fc > Delivery options: > https://carpentries.topicbox.com/groups/discuss/subscription > ------------------------------------------ The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/T45d1f9e935d7181b-M980cec25c470756c12243316 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
