Anatomy of an Open Science Paper

We use lab notebooks to record research. Why not publish lab notebooks alongside papers?

My lab just published a paper on some chemical methodology towards some potential tuberculosis drugs we finished last year. The chemistry was carried out by Kat Badiola, with bio testing courtesy of my colleague Jamie Triccas at Sydney Uni.

In some senses it’s a traditional paper, but it has an interesting feature.

Standard, brief papers are like press releases, conveying the choicest bits of the science. Most manuscripts we often read are a little like this.

Which is useful but of course ridiculous – like icing with no cake. So we often prefer to publish larger pieces of work, where the choicest bits are accompanied by a “Supporting Information” section – stuff you consult if you want to know more. Usually this is a PDF file, usually containing pictures of datasets – in Chemistry this is usually copies of NMR spectra, for example.

Which is also ridiculous on its own, since it’s 2014 and megabytes are cheaper than milk now, so we’re able to include raw data files too (though people seldom do, I don’t know why) and we’ve done so with this paper. So you can download the files and reprocess spectra for yourself if you like. Useful for all sorts of obvious reasons I won’t list here.

Which is great but not enough.

What about all the “failed” reactions? What about the repeats, so that one can assess reproducibility? What about the comments and ideas we all put in lab notebooks, such as things to try next? What about the strands of the projects that didn’t quite work out, but may yield to another investigator? What about photos of the science (genuinely useful in organic synthesis), or other data that would help someone wanting to take this research on?

In other words, wouldn’t it be useful to include the lab notebook as part of the paper?

That’s what we’ve done here. The electronic lab notebook Kat used – it’s been zipped up and put on our Uni’s institutional repository. You can download it, unzip it and explore it as a snapshot using a web browser – all the links work, and every experiment is in there.

Components of a Paper

Components of a Paper

Useful, and easy to do. Very easy for open projects, since you are already sharing everything so why not zip up the notebooks and include them? It’s probably more difficult for closed projects only because if a lab notebook is closed it’s probably not necessarily in the best shape to be shared with others – openness in record keeping can encourage (not guarantee) a way or recording activity that is understandable by others outside the team. Including the notebook is essentially impossible if you’re still using a paper lab notebook (for shame!)

Thanks to the Labtrove team at the Uni of Southampton for capturing the snapshot and generally being great.

(Related links: Some suggestions as to how we might change journal articles in future are here. More on the browser-based notebook Labtrove here and here. Please comment below if I’ve missed anything.)