Home » Blog

Notes from Scifoo

11 August 2008 4 Comments

I am too tired to write anything even vaguely coherent. As will have been obvious there was little opportunity for microblogging, I managed to take no video at all, and not even any pictures. It was non-stop, at a level of intensity that I have very rarely encountered anywhere before. The combination of breadth and sharpness that many of the participants brought was, to be frank, pretty intimidating but their willingness to engage and discuss and my realisation that, at least in very specific areas, I can hold my own made the whole process very exciting. I have many new ideas, have been challenged to my core about what I do, and how; and in many ways I am emboldened about what we can achieve in the area of open data and open notebooks. Here are just some thoughts that I will try to collect some posts around in the next few days.

  • We need to stop fretting about what should be counted as ‘academic credit’. In another two years there will be another medium, another means of communication, and by then I will probably be conservative enough to dismiss it. Instead of just thinking that diversifying the sources of credit is a good thing we should ask what we want to achieve. If we believe that we need a more diverse group of people in academia than that is what we should articulate – Courtesy of a discussion with Michael Eisen and Sean Eddy.
  • ‘Open Science’ is a term so vague as to be actively dangerous (we already knew that). We need a clear articulation of principles or a charter. A set of standards that are clear, and practical in the current climate. As these will be lowest common denominator standards at the beginning we need a mechanism that enables or encourages a process of incrementally raising those standards. The electronic Geophysical Year Declaration is a good working model for this – Courtesy of session led by Peter Fox.
  • The social and personal barriers to sharing data can be codified and made sense of (and this has been done). We can use this understanding to frame structures that will make more data available – session led by Christine Borgman
  • The Open Science movement needs to harness the experience of developing the open data repositories that we now take for granted. The PDB took decades of continuous work to bring to its current state and much of it was a hard slog. We don’t want to take that much time this time round – Courtesy of discussion led by Sarah Berman
  • Data integration is tough, but it is not helped by the fact that bench biologists don’t get ontologies, and that ontologists and their proponents don’t really get what the biologists are asking. I know I have an agenda on this but social tagging can be mapped after the fact onto structured data (as demonstrated to me by Ben Good). If we get the keys right then much else will follow.
  • Don’t schedule a session at the same time as Martin Rees does one of his (aside from anything else you miss what was apparently a fabulous presentation).
  • Prosthetic limbs haven’t changed in 100 years and they suck. Might an open source approach to building a platform be the answer – discussion with Jon Kuniholm, founder of the Open Prosthetics Project.
  • The platform for Open Science is very close and some of the key elements are falling into place. In many ways this is no longer a technical problem.
  • The financial system backing academic research is broken when the cost of reproducing or refuting specific claims rises to 10 to 20-fold higher than the original work. Open Notebook Science is a route to reducing this cost – discussion with Jamie Heywood.
  • Chris Anderson isn’t entirely wrong – but he likes being provocative in his articles.
  • Google run a fantasticaly slick operation. Down to the fact that the chocolate coated oatmeal biscuit icecream sandwiches are specially ordered in made with proper sugar instead of hugh fructose corn syrup.

Enough. Time to sleep.


  • Regarding guidelines: I suggested in http://pyre.third-bit.com/blog/archives/1677.html that something like the Open Source Initiative’s certification would be useful.

  • Regarding guidelines: I suggested in http://pyre.third-bit.com/blog/archives/1677.html that something like the Open Source Initiative’s certification would be useful.

  • Hi Greg, I missed that original blog post of yours but that is indeed exactly what we are trying to evolve so as to get an initial working draft out of PSB (or at least the structural outlines of such a thing). As deepak says in the comments to your post we will need to be very careful about minimum standards – further blog post on this will be forthcoming as soon as I can get myself back into the right timezone (probably just about in time for me to got to Waterloo!)

  • Hi Greg, I missed that original blog post of yours but that is indeed exactly what we are trying to evolve so as to get an initial working draft out of PSB (or at least the structural outlines of such a thing). As deepak says in the comments to your post we will need to be very careful about minimum standards – further blog post on this will be forthcoming as soon as I can get myself back into the right timezone (probably just about in time for me to got to Waterloo!)