Research Remix

July 18, 2007

ISMB 2007 BoF: Open (Notebook) Science

Filed under: BOF, ISMB, openscience — Heather Piwowar @ 10:11 am

There will be a Birds of a Feather session at ISMB 2007 about Open (Notebook) Science.  It was initiated by yours truly, not because I’m an expert (I’m not!) or even because I have any real experience doing Open Notebook Science (I don’t!), but because I’d like to meet others who are interested and have a good conversation.  Sounds like a BoF to me!

So if you are at ISMB and available Wednesday at lunch, stop on by.

ps Thanks to Bill Hooker for his great summary, and to
all these people blogging about the Open Science Notebook [neat], and especially all those people who are really doing it.

Description: Open (Notebook) Science — the practice
of freely and openly sharing the process, data, tools, and results of
our research — is gaining momentum. For a nice overview, see
BOF for people doing, considering, or curious about Open Science.

Also note another BoF of interest, on Tuesday:
Data and Software Sharing     
Barb Bryant   
[Vice President of
the International Society for Computation Biology (ISCB)]

This session will explore options for Data and Software Sharing and is open to all to provide feedback to ISCB.

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  1. About that summary: it’s CC-BY, and I promise I will label it as such *asap*. (I keep meaning to and forgetting; I suck.) So you can do anything you like with it. It’s only BY instead of Pub Dom because I want 3QuarksDaily to get whatever publicity it might generate.

    And thank you for convening the Open Notebook session! The more exposure these (Open Foo) ideas get, the better.

    Comment by Bill — July 18, 2007 @ 12:18 pm

  2. Heather – just to clarify what I intended with the use of the term “Open Notebook Science”:

    To clear up confusion, I will use the term Open Notebook Science, which has not yet suffered meme mutation. By this I mean that there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

    Anything less than this may still be a form of Open Science but is not ONS. One of the behaviors that concerns me is the selective release of scientific information. If research is ONS you should show absolutely everything (including failed attempts) in your official laboratory notebook and linked raw data.

    Good luck with the meeting and I look forward to hearing about how it went!

    Comment by Jean-Claude Bradley — July 19, 2007 @ 7:52 am

  3. Thank you, that is very helpful. The distinction wasn’t clear to me before.

    A few follow up questions I’ve been curious about. For you, does ONS also necessitate that you release everything quickly? As in within hours/days of running the experiments, or within weeks/months?

    Does it also extend to releasing meeting notes and ideas from future projects, as they occur to you? So not just the methods and data, but also the advance and reflective thinking? Or would you consider this nice but not key?

    I know I will have more questions for you, and I’m looking forward to reading your website, Nature Precedings posting, etc. in more detail.

    Thanks so much for leading the way!

    Comment by Heather Piwowar — July 19, 2007 @ 9:02 am

  4. Heather,
    The timeliness is a very good point. The policy in my lab is that all of the Log sections of experiments have to be updated at the very latest by the end of that day:

    Results, Discussion and Conclusion can be done later as we process the raw data and consult the literature. I think that is pretty common for any laboratory notebook, paper or electronic.

    If the lab had a private notebook updated immediately then a public one with different content or released at a later time I would not consider that ONS.

    The access to the notebook must be completely open to humans and machines (no login for example).

    I think that makes for a fairly objective definition of the term.

    The question of including ideas, future projects and other forms of communication extends the concept of sharing to something I usually refer to as Completely Transparent Science. With humans this is an ideal that cannot be reached realistically – you would have to include every conversation and every unrecorded thought. There are logistical problems with that and some difficulty with respecting privacy issues.

    I do my best to record these thoughts (hypotheses, milestones, etc.) on our main blog and link back to the laboratory notebook for access to the raw data:

    I have found recently that the use of a mailing list can keep a fairly good record of the small details that don’t show up on the blog or wiki, especially with external collaborations:

    Hope thats makes it clearer. I look forward to your next study on trying to qualify and quantify what is happening in the world of “Open Science”.

    Comment by Jean-Claude Bradley — July 19, 2007 @ 2:52 pm

  5. […] Filed under: ISMB, BOF — Heather Piwowar @ 4:58 am In anticipation of the ISMB BoF session on Open Notebook Science (ONS), I’m trying to come up to speed on ONS discourse.  In between ISMB sessions, […]

    Pingback by Messy Notes on Open Notebook Science « Research Remix — July 24, 2007 @ 4:58 am

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