Want a permanent DOI assigned to your data and code? Follow this simple recipe

2 11 2021

These days with data and code often required to be designated as open-source, licenced, and fully trackable for most manuscript submissions to a peer-reviewed journal, it’s easy to get lost in the multitude of platforms and options available. In most cases, we no longer have much of a choice to do so, even if you are reticent (although the benefits of posting your data and code online immediately far outweigh any potential disadvantages).

But do you post your data and code on the Open Science Framework (free), Github (free), Figshare (free), Zenodo (free, but donations encouraged), Dryad ($), or Harvard Dataverse (free) (and so on, and so on, …)? Pick your favourite. Another issue that arises is that even if you have solved the first dilemma, how do you obtain a digital object identifier (DOI) for your data and/or code?

Again, there are many ways to do this, and some methods are more automated than other. That said, I do have a preference that is rather easy to implement that I’d thought I’d share with you here.

The first requirement is getting yourself a (free) Github account. What’s Github? Github is one of the world’s largest communities of developers, where code for all manner of types and uses can be developed, shared, updated, collaborated, shipped, and maintained. It might seem a bit overwhelming for non-developers, but if you strip it down to its basics, it’s straightforward to use as a simple repository for your code and data. Of course, Github is designed for so much more than just this (software development collaboration being one of the main ones), but you don’t need to worry about that for now.

Step 1

Once you create an account, you can start creating ‘repositories’, which are essentially just sections of your account dedicated to specific code (and data). I mostly code in R, so I upload my R code text files and associated datasets to these repositories, and spend a good deal of effort on making the Readme.md file highly explanatory and easy to follow. You can check out some of mine here.

Ok. So, you have a repository with some code and data, you’ve explained what’s going on and how the code works in the Readme file, and now you want a permanent DOI that will point to the repository (and any updates) for all time.

Github doesn’t do this by itself, but it integrates seamlessly with another platform — Zenodo — that does. Oh no! Not another platform! Yes, I’m afraid so, but it’s not as painful as you might expect.

Read the rest of this entry »




Why do they take so long?

4 05 2018

phd1This is probably more of an act of self-therapy on a Friday afternoon to alleviate some frustration, but it is an important issue all the same.

An Open Letter to academic publishers:

Why, oh why, do some of you take so bloody long to publish our papers online after acceptance?

I have been known to complain about how the general academic-publishing industry makes sickening amount of profit on the backs of our essentially free labour, and I suppose this is just another whinge along those lines. Should it take weeks to months to publish our papers online once they are accepted?

No. it shouldn’t.

I’m fully aware that most publishing companies these days outsource the actual publishing side of things to subcontracting agencies (and I’ve noticed more and more that these tend to be in developing nations, probably because the labour is cheaper), and that it can take someone some time to work through the backlog of Word or Latex documents and produce nice, polished PDFs. Read the rest of this entry »





Ecologists: join F1000Research’s open science ecosystem

8 08 2013

f1000researchlogoThe people at the new open-access journal F1000Research (a Faculty of 1000 publication) have asked me to help them announce their new deal for ecologists – no processing fees until 2014! Might have to give it a go myself…

F1000Research covers all areas of life sciences, but we know that different fields each have their own unique characteristics, and some features of our journal are of particular interest to certain disciplines.

For the coming months, one area we’ll be focussing on is ecology. To encourage ecologists to try F1000Research, we’re waiving the article processing charge for all first submissions of an ecology paper until 2014. (Use code ECOL15 when submitting).

F1000Research is an ideal venue for publishing an ecology paper. Research, which includes full datasets, is openly available and its speed of publication and transparency in reviews makes it a refreshing alternative to traditional publishing.” Gary Luck, Institute for Land, Water and Society, Charles Sturt University, Australia

Three good reasons to send your ecology papers to F1000Research:

1.     Quickly reach a wide audience

All articles are fully open access and include all data, and with our post-publication peer review model, your article can be online within a week (find out more about our speedy publication process). Read the rest of this entry »








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