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January 11, 2017 / Damien Irving

Need help with reproducible research? These organisations have got you covered.

The reproducibility crisis in modern research is a multi-faceted problem. If you’re working in the life sciences, for instance, experimental design and poor statistical power are big issues. For the weather, ocean and climate sciences, the big issue is code and software availability. We don’t document the details of the code and software used to analyse and visualise our data, which means it’s impossible to interrogate our methods and reproduce our results.

(For the purposes of this post, research “software” is something that has been packaged and released for use by the wider community, whereas research “code” is something written just for personal use. For instance, I might have written some code to perform and plot an EOF analysis, which calls and executes functions from the eofs software package that is maintained by Andrew Dawson at Oxford University.)

Unbeknown to most weather, ocean and climate scientists, there are a number of groups out there that want to help you make your work more reproducible. Here’s a list of the key players and what they’re up to…

 

Software Sustainability Institute (SSI)

The SSI is the go-to organisation for people who write and maintain scientific software. They provide training and support, advocate for formal career paths for scientific software developers and manage the Journal of Open Research Software, where you can publish the details of your software so that people can cite your work. They focus mainly on researchers in the UK, so it’s my hope that organisations like SSI will start popping up in other countries around the world.

 

OntoSoft

The OntoSoft project in the US has a bit of overlap with the SSI (e.g. they’re working on “software commons” infrastructure where people can submit their geoscientific software so that it can be searched and discovered by others), but in addition their Geoscientific Paper of the Future (GPF) initiative has been looking at the broader issue of how researchers should go about publishing the details of the digital aspects of their research (i.e. data, code, software and provenance/workflow). In a special GPF issue of Earth and Space Science, researchers from a variety of geoscience disciplines share their experiences in trying to document their digital research methods. The lead paper from that issue gives a fantastic overview of the options available to researchers. (My own work in this area gives a slightly more practical overview but in general covers many of the same ideas.)

 

Software Carpentry

The global network of volunteer Software Carpentry instructors run hundreds of two-day workshops around the world each year, teaching the skills needed to write reusable, testable and ultimately reproducible code (i.e. to do the things suggested by the GPF). Their teaching materials have been developed and refined for more than a decade and every instructor undergoes formal training, which means you won’t find a better learning experience anywhere. To get a workshop happening at your own institution, you simply need to submit a request at their website. They’ll then assist with finding local instructors and all the other logistics that go along with running a workshop. A sibling organisation called Data Carpentry has recently been launched, so it’s also worth checking to see if their more discipline-specific, data-centric lessons would be a better fit.

 

Mozilla Science Lab

Once you’ve walked out of a two-day Software Carpentry workshop, it can be hard to find ongoing support for your coding. The best form of support usually comes from an engaged and well connected local community, so the Mozilla Science Lab assists researchers in forming and maintaining in-person study groups. If there isn’t already a study group in your area, I’d highly recommend their study group handbook. It has a bunch of useful advice and resources for getting one started, plus they periodically run online orientation courses to go through the handbook content in detail.

 

Hopefully one or more of those organisations will be useful in your attempts to make your work more reproducible – please let me know in comments if there’s other groups/resources that I’ve missed!

 

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2 Comments

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  1. heylsitan / Feb 23 2017 12:44

    authorea is not free now, which is a little expensive for graduate student.

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