What Is Your Notebook?

Here at Scimatic, we follow both Greg Wilson and Cameron Neylon on Twitter, so it was cool to see the two of them talking about the directions of Open Science in a semi-public forum. The tweet that caught my eye was

and I have to agree with this. I get the sense there is a framework to deal with how to share data, and there is a healthy debate on when to share data, from "the moment you record it," to "when you publish the paper," to "never." I tend to fall into the "when you publish the paper camp," but I'm glad we're having the discussion. Cameron provided more than 140 characters of information about what he sees as the next steps in a very informative interview:

Open Notebook Science is two things: a process and a commitment. The commitment is that you make your best effort to make the full record of your research available as you record it; i.e. as close as possible to as it happens. In a sense this is an ideal rather than something that is practically achievable. There are always variables that you don’t record, indeed don’t think to record, the “unknown unknowns” of research. But the point is that you do the best that is feasible with the resources you have – at a minimum making sure that the record that you use and make is the one that is available to the rest of the world.

[Emphasis mine.]

I have concerns that this is not feasible in the current academic climate. The currency of academics is publications; those, coupled with recommendations, is how people get jobs. And the downside of that fact is that there is the possibility if you put your research into the wild too early, you will get scooped. At the Science 2.0 conference in Toronto this year, there were a number of good talks about how to mitigate this problem, either through licensing or changes to the culture. But I feel we're 20 years away from having that change go through.

However, one place where we can change now is how scientists record their science. Cameron wants all your notebooks on a public website. Like I said above, I don't think this feasible in today's academic climate. However, one thing that isn't controversial is that the old style pen and paper notebook just won't cut it for the upcoming needs of shared science. For example, there were a set of papers that were retracted recently because the research group could not find the paper notebooks that contained the research detailed.

When I started research, I loved using the fancy lab notebooks. These ones from leather bound ones from Boorum & Pease seemed so official and important. Clearly I was now doing Real Science that would be Preserved for Posterity. However, I soon realized they weren't really what I needed. They can't be searched, indexed or tagged. And most importantly, for the type of science I did, you couldn't actually store the data in them. You could only make written reference to the data files that were stored somewhere else.

And that is the problem with the venerable lab notebook. The data has moved somewhere else, and where that somewhere else is depends on the scale of the experiments. For desktop experiments, the data might be stored in XML, a spreadsheet, or a binary data format read out from a lab machine. For larger experiments, such as bioinformatics and large scale physics experiments, the data are stored on a central repository somewhere where you have to request access or submit analysis computational jobs to repository to access the data. Our friend the @mza has a set of online talks about the challenges related to the petabyte scale of data analysis. Along with the data, the papers and references have also moved online. Researchers need to be able to link all that information together.

Electronic lab notebooks (ELNs) are popular in commercial scientific research, such as pharmaceuticals. Most of the ELNs I found in a quick search are "enterprise" level solutions, meant for large groups or companies, with a matching "enterprise" cost, to the point where none of those listed companies put their price list online. If you have to ask, you probably can't afford it.

However, back to your notebook. It feels to me like the ELN is coming to the single researcher/small group pretty quickly, where you can integrate your procedures, notes and references to your data all in one. We here at Scimatic have some definite ideas on how an ELN should look, and we've just released Samples to fill that need. In Samples, you can manage your experiments, procedures, samples, observations and results. Instead of writing "observations about dataset ds010.0", you write "observations about dataset  ds010.0" with the built-in link to the data. Your notes are searchable and indexed, so that when you come back six months from now, you can figure out what you were doing. More importantly, when someone else in your lab comes back to reproduce your work, they can find it too, thus avoiding a retraction problem.

We think there is huge potential for simple and easy to use electronic lab notebooks. In the same way that 37 Signals went for simple and "less is more" with their project management and CRM tools, there's a lot of space for new ELNs that compete, not with the "enterprise" solutions, but with the venerable pen'n'paper notebook. We think that once you try Samples, you will agree.