Summary of ONS BoF at ISMB

Back at home after a lovely cycling vacation along the Danube with my family.

Quick summary of the Birds of a Feather on Open Notebook Science (ONS) at ISMB:

The session was during a short lunchtime on the last day, thus not ideal for high attendence.  Nonetheless, about 10 young scientists attended (including Frank and Matt, what fun to meet in person), and we had an interesting discussion.

• many of us, but not all, had heard of ONS previously.  Nobody doing it.
• challenges specific to bio/biomed/informatics:
• sharing details about invasive animal experiments on the open internet could (and has) lead to harassment
• privacy issues with clinical data (comment:  would first be fired then sued)
• maybe ways around this, share lots but not everything, model how it is handled in publications, etc
• general points:
• more “errors” are bound to be found, will need a new publishing paradigm to deal with this
• process for assessing research is disjoint from these practices, though changes are underway
• only valid in areas where no potential commercial benefit, otherwise universities won’t allow?
• might encourage informal peer review, thus raising the quality of  submissions and helping the investigators
• young investigators just can’t risk being scooped
• time-marked stake in the sand a reasonable defense?  Parallels with patent law.
• will need social change
• fear of scooping perhaps more pervasive than it occurring
• yet a first-hand example in the room of being scooped from a rejected grant application
• flip side:  if someone realizes that other good investigators are already working on something and n months ahead, they may forgo it and do something else
• flip side:  potential collaborations
• thoughts that the benefits may start outweighing the risks after the work is already well underway, as opposed to just being started
• at the end of the session (generalizing) most in the room felt that ONS is interesting to think about, hard to pull off, perhaps possible as small steps, social change required.

Thanks to everyone who attended.  I enjoyed meeting you, and learned from the different perspectives in the conversation.

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Messy Notes on Open Notebook Science

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, I’ve started consolidating snippets of blog
posts and articles discussing ONS into a single document (in the open here).  It obviously relies heavily on work from Bill Hooker and Jean-Claude Bradley:  Thank you.   Following the advice to
“make a mess in your zero draft,” the current version isn’t very good
reading.  I have many more links to comb, and then I’ll start pulling it
together and making a first-draft (aka human-readable version).  I’ll
post again once it gets to that state.

ISMB 2007 BoF: Open (Notebook) Science

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.

Details:
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
http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html.
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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BOF: Online distribution of scientific research

Paris, springtime, and a birds-of-a-feature session about sharing research data online. Does it get any better than that?!?  I’d love to go…

Excerpted from XTech 2007:

Online distribution of scientific research

Gavin Bell (Nature), Alf Eaton (Nature)

17:30 Tuesday May 15

BOF Amphitheatre A

This BOF session will cover several themes important to those developing and promoting tools for scientific research, collaboration and publishing online.

1. Identifiers and Identity: To be able to combine research on information from disparate sources, topics need to be clearly identified: molecules, documents, authors and data all need identifiers. What are the successful initiatives in this area, how have they succeeded and what’s still needed?
2. Documents and Datasets: Openness, access to and re-use of results. Storage and distribution of datasets, large and small. The future of document formats for publishing the results of scientific research online.
3. Collaboration, Contribution and Credit: Developing tools for constant data sharing and discussion while research is in progress, rather than much later when the work is finished. Credit for contributions outside the traditional sphere of academic publishing.

If you’re interested in these topics and able to attend, please email Alf Eaton a.eaton@nature.com so we can get an idea of preferences — or feel free to attend anyway.

Thanks to Alf Eaton at HubLog for the link.