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BioBarCamp – Meeting friends old and new and virtual

7 August 2008 14 Comments

So BioBarCamp started yesterday with a bang and a great kick off. Not only did we somehow manage to start early we were consistently running ahead of schedule. With several hours initially scheduled for introductions this actually went pretty quick, although it was quite comprehensive. During the introduction many people expressed an interest in ‘Open Science’, ‘Open Data’, or some other open stuff, yet it was already pretty clear that many people meant many different things by this. It was suggested that with the time available we have a discussion session on what ‘Open Science’ might mean. Pedro and mysey live blogged this at Friendfeed and the discussion will continue this morning.

I think for me the most striking outcome of that session was that not only is this a radically new concept for many people but that many people don’t have any background understanding of open source software either which can make the discussion totally impenetrable to them. This, in my view strengthens the need for having some clear brands, or standards, that are easy to point to and easy to sign up to (or not). I pitched the idea, basically adapting from John Wilbank’s pitch at the meeting in Barcelona, that our first target should that all data and analysis associated with a published paper should be available. This seems an unarguable basic standard, but is one that we currently fall far short of. I will pitch this again in the session I have proposed on ‘Building a data commons’.

The schedule for today is up as a googledoc spreadsheet with many difficult decisions to make. My current thinking is;

  1. Kaitlin Thaney – Open Science Session
  2. Ricardo Vidal and Vivek Murthy (OpenWetWare and Epernicus).  Using online communities to share resources efficiently.
  3. Jeremy England & Mark Kaganovich – Labmeeting, Keeping Stalin Out of Science (though I would also love to do John Cumbers on synthetic biology for space colonization, that is just so cool)
  4. Pedro Beltrao & Peter Binfield – Dealing with Noise in Science / How should scientific articles be measured.
  5. Hard choice: Andrew Hessel – building an open source biotech company or Nikesh Kotecha + Shirley Wu – Motivating annotation
  6. Another doozy: John Cumbers – Science Worship / Science Marketing or Hilary Spencer & Mathias Crawford – Interests in Scientific IP – Who Owns/Controls Scientific Communication and Data?  The Major Players.
  7. Better turn up to mine I guess :)
  8.  Joseph Perla – Cloud computing, Robotics and the future of Science and  Joel Dudley & Charles Parrot – Open Access Scientific Computing Grids & OpenMac Grid

I am beginning to think I should have brought two laptops and two webcams. Then I could have recorded one and gone to the other. Whatever happens I will try to cover as much as I can in the BioBarCamp room at FriendFeed, and where possible and appropriate I will broadcast and record via Mogulus. The wireless was a bit tenuous yesterday so I am not absolutely sure how well this will work.

Finally, this has been great opportunity to meet up with people I know and have met before, those who I feel I know well but have never met face to face, and indeed those whose name I vaguely know (or should know) but have never connected with before. I’m not going to say who is in which list because I will forget someone! But if I haven’t said hello yet do come up and harass me because I probably just haven’t connected your online persona with the person in front of me!


  • On your comment that “all data and analysis associated with a published paper should be available. This seems an unarguable basic standard, but is one that we currently fall far short of” – there is an often overlooked ‘declaration’ by the STM Publishers Group – The Brussels Declaration – http://www.stm-assoc.org/brussels-declaration/ which specifically states that “Raw research data should be made freely available to all researchers. Publishers encourage the public posting of the raw data outputs of research. Sets or sub-sets of data that are submitted with a paper to a journal should wherever possible be made freely accessible to other scholars”.

    To my knowledge, not too many people are aware of this declaration and this clause, and certainly I believe that the majority of signatories are not enforcing it.

    Pete Binfield

  • On your comment that “all data and analysis associated with a published paper should be available. This seems an unarguable basic standard, but is one that we currently fall far short of” – there is an often overlooked ‘declaration’ by the STM Publishers Group – The Brussels Declaration – http://www.stm-assoc.org/brussels-declaration/ which specifically states that “Raw research data should be made freely available to all researchers. Publishers encourage the public posting of the raw data outputs of research. Sets or sub-sets of data that are submitted with a paper to a journal should wherever possible be made freely accessible to other scholars”.

    To my knowledge, not too many people are aware of this declaration and this clause, and certainly I believe that the majority of signatories are not enforcing it.

    Pete Binfield

  • peter, thanks for that – I was totally unaware of this, which may well be just down to my ignorance, but it is very worth knowing. Again though I would draw a distinction between the idea that the author should have it on a hard disk and make it available on request and it being truly available.

    This is at the core of defining a standard though – what do we mean by ‘accessible’. Can we pitch a redefined standard to the next such convention?

  • peter, thanks for that – I was totally unaware of this, which may well be just down to my ignorance, but it is very worth knowing. Again though I would draw a distinction between the idea that the author should have it on a hard disk and make it available on request and it being truly available.

    This is at the core of defining a standard though – what do we mean by ‘accessible’. Can we pitch a redefined standard to the next such convention?

  • Cameron,

    I have bee enjoy reading, watching and reliving BioBarCamp all morning. Thank you for doing this!

  • Cameron,

    I have bee enjoy reading, watching and reliving BioBarCamp all morning. Thank you for doing this!

  • Possibly. An industry group of some sort (even if not STM) would be the best way to make it happen consistently.

  • Possibly. An industry group of some sort (even if not STM) would be the best way to make it happen consistently.

  • Took a peek at yr mogulus but couldn’t find any recorded stuff.
    If you have / find any recorded stuff from the event (pref audio/.mp3) pls share the links!

    Hoping to help you / richard grant do likewise for Nature’s science blogging event in london at the end of the month.

    Take care
    Fang – Mike Seyfang

  • Took a peek at yr mogulus but couldn’t find any recorded stuff.
    If you have / find any recorded stuff from the event (pref audio/.mp3) pls share the links!

    Hoping to help you / richard grant do likewise for Nature’s science blogging event in london at the end of the month.

    Take care
    Fang – Mike Seyfang

  • Mike, you should be able to get to them by clicking on ‘on demand’ button at the bottom of the viewing window. It seems to be working at the moment but it wasn’t until I had logged back in which seems wierd. Hopeully keep working for the moment. if someone wants to screen capture the video feel free.

  • Mike, you should be able to get to them by clicking on ‘on demand’ button at the bottom of the viewing window. It seems to be working at the moment but it wasn’t until I had logged back in which seems wierd. Hopeully keep working for the moment. if someone wants to screen capture the video feel free.

  • Great blog Cameron! Enjoyed meeting you at BioBarCamp and discussing your lab management software. Prasanth and I had quite a brainstorming session on our trip home imagining how we could utilize something similar.

  • Great blog Cameron! Enjoyed meeting you at BioBarCamp and discussing your lab management software. Prasanth and I had quite a brainstorming session on our trip home imagining how we could utilize something similar.