Putting reproducible research papers online

Reproducible Research
OK, you’ve made a reproducible research (RR) paper. How to make it available online?

At LCAV, we started off by simply making an HTML web page with all the paper details and additional information (data, code, additional figures), and putting that on our lab website.

While this is a very straightforward way of working, it is probably not very practical in the long term, as a new web page has to be made for each new publication. I can also imagine writing HTML may seem a big step (or just too cumbersome) to some. That’s why we have developed, in collaboration with the EPrints team, a Reproducible Research Repository setup. It has to be configured once (by your system administrator?), and allows you then to upload new RR papers by filling out a form with all the necessary information and uploading PDF, code, data, and/or any other additional material. I think it is really a lot more user-friendly than creating HTML pages each time. At the same time, it assures that all the information is there, and creates nice web pages (see here for an example of the repository front page, and here for an example of a page for a paper).

The setup of such a server should be really easy to do. You start off with a standard installation of EPrints, which requires rather standard web server tools: Apache (with mod_perl), MySQL and Perl. EPrints is a digital repository software that is widely used to set up (institutional) publications repositories. Once you have installed this, the most difficult part is already done (and it really is not that difficult to install). Follows only a configuration to add the possibility of adding code/data. Finally, on the same page, I also described all the formatting modifications we did to the LCAV site.

Next to the possibility of adding code, data and additional material, we also added a few other features (see here for an example). First of all, you can add a describing figure to your paper (under the motto “a figure says more than a thousand words”?). And then, more importantly, we also added the possibility for readers to leave comments and a user evaluation. In this way, readers of your paper can evaluate how reproducible it is, and tell that to other potential readers. Kind of a review-after-the-review…

In parallel with these developments, Patra Pantupat, Aliaksei Sandryhaila, and Markus Pueschel developed The Pub, another setup supporting reproducible research. More information can be found here.

Voila, I think that’s the most important about our repository setup. I hope it will be useful to you!

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