Towards Universal Online Laboratory Notebooks – in theory

onlinelabnotebooksMaxine Clarke, Nature’s blogactive and web-oriented Publishing Executive Editor blogged on has an interesting and opinionated editorial on Share your lab notes in Nature 447, 1-2 (3 May 2007). also available at Nautilus.

Her The line of argument is: The use of electronic laboratory notebooks should be supported by all concerned since they “contain data that flow automatically from lab instruments and can be read by all lab members”. This availability to other collaborators should compel the keeping of better records. Most importantly: “If each notebook is allocated a unique identifying code — a permanent alphanumeric string containing information about provenance, creation dates and digital location — it can be cited in journals as a confirmation that the data are safely stored, ultimately available and sharable (with due regard for the rights of the researchers involved). It also confirms that the original data can be retrieved in the case of errors or accusations of fraud.” This way, Clarke the editorial goes on, both “the rigour and transparency of publicly funded research will be improved”.

And she the author of the editorial is absolutely right. But there are many, geographically distant interlab collaborations too, not just intralab projects in the vicinity of 2 rooms on the same floor. Let’s put these ideas into context to see them live.

I’d like to step further a little bit as Clarke the author of the editorial misses to consider the current technological situation: all these nice aims, the standardization (unique URL to every lab notebook), the universal, collaborative sharing of digital notebooks could obviously be realizable by web-based applications (Google Docs, collaborative wikis) rather than Office-like desktop softwares and restricted local networks.

Or more dynamically: can you imagine individual experiments as blog posts, and a lab notebook as a project blog? After all, every experiment has a principal investigator, and all the other participators could be interpreted as commenters. Or this is not the case (we need a group blog in case when the FACS measurement at the end of my cell culture experiment is implemented and recorded by another scientist), and more democratic wikis are the real solutions? Who knows it yet? But the direction is clear. Webtop apps.

16 thoughts on “Towards Universal Online Laboratory Notebooks – in theory

  1. There’s also the problem of only being able to publish unique experiments. Many (most?) journals consider anything on the internet as published and therefore they need to change their rules before open notebooks will be able to really take off.

  2. I don’t see how open laboratory notebooks are that different from pre-print archives (like arXiv in physics) that many publishers now accept. But even if most publishers don’t accept this, that is not a problem – we only need one in a given field.

  3. Thanks for the link, Attila. I should just point out that I’m not the author of the article. The article is an Editorial in Nature which I featured on Nautilus as that is where we ask scientists to comment on policy issues before we decide whether or not to make something a policy — eg data availability.
    I like the Google docs&spreadsheets idea, though!

  4. PS to Jean-Claude — Nature and the other Nature journals are all very happy for authors to use the arXive preprint system. Are there any other preprint servers that are indexed properly as ArXive is? I don’t think I know of any.

  5. Oops, sorry for falsely attributing the editorial to you, Maxine and thanks for the correction, it is corrected. May we know who was the author? Or it is a policy on editorials representing an editorial consent on a policy, that the author is hidden and the reader might only guess.

  6. Preprint problems: well, I am planning to publish my old results (at that time in 1999 quite new) on mitochondrial DNA promoter mutations in aged persons’ brain in this very blog, not in ArXive but I am hesitating due to the peer review publishing principles. Is there any precedent that a draft was not accepted as the results were previously published on a blog? I think it’s time now to study Nature’s own open peer-review trial.

  7. Maxine,
    Yes, in addition to arXiv, I am referring to self-archiving on institutional repositories, like DSpace or iDea. A few weeks ago, one of our librarians gave us a presentation showing examples of chemistry articles already available on our institutional repository before actual publication in the journal (sorry I don’t remember the journal in this case but she had a list of them). From what I understood, the rules for institutional repositories are different from just anyone reproducing an article before or after publication. I think they were allowed to reproduce all the text and figures but not in an identical format to how it would appear in the journal. Maybe you can tell us more about Nature’s self-archiving policy.

    Attila, I don’t know of a case where disclosure of primary data on a blog prevented publication but it is clearly a violation of written terms of submission for many journals. However, I have found that editors can override that on request. Right now I am trying to get such an override from an ACS journal that asked me to write an article that I want to write on a wiki first.

    And lets keep in mind that there are 2 different issues here – the publication of laboratory notebook pages with raw data and failed experiments and the pre-publication of completed articles before submission to a journal. We are doing both.

  8. This is, in general, a fantastic idea, provided you have the technical ability to make it work for you with a minimum of start-up and messing about. Blogging apps like WordPress already provide for publicly visible/privately visible content and group contributions. A wiki and forum can be useful adjuncts, but I would imagine that a full-on wiki is overkill for most things, which could be more easily handled with a link to a static page.

    As far as actual presentation of the data goes, visualization skills are essential. Are you familiar with the Simile project, particularly Exhibit? As Johan Sundström says, it’s the recipe for innovation.

  9. Mr. Gunn,
    I agree that simplicity is absolutely key to enabling the technology to be used by researchers. For most chemists that I know (including my students), creating a static web page is much more difficult that using a wiki. HTML is intimidating for many people.

    The Exhibit technology that you mention does look like it could be useful but it does require coding, even though as the tutorial says, mainly copying and pasting. We have looked at visualization technology that does not require coding, like ManyEyes.

  10. Jean-Claude: prepublishing a review not an original article with new data on a blog also counts as a violation of written terms of submission?

    Wiki, blog, static html platform technological question: in october, 2006 I set up a blog and a wiki for a conference, Stem Cells in Tissue Engineering Conference: Blog and Wiki and emailed the addresses to every conference participants before launching the conference, but unfortunately there was only a minimal participation in them.

  11. Attila,
    Getting other scientists to contribute to wiki projects is very difficult indeed. I think the key at this point in time is to find those few people who see the validity of making these contributions self-evident and work hard with them to make it happen.

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