Special Session 4: Panel Session (ISMB 2009)

Panel Session with the three previous speakers plus Philip Bourne, Editor-In-Chief PLoS Computational Biology
Part of the Advances and Challenges in Computational Biology, hosted by PLoS Computational Biology

Changing the scientific culture to increase collaboration. How to make it easy to collaborate? Make it easy / required to submit work in a standard way to a journal, perhaps?

  • AA: the problem is reward. The reward for publishing a model as SBML is zero, or even negative right now. Until it stops “preventing” us from doing science (e.g. doing stuff we don’t “have to” do), you won’t see as much an uptake as you should. Even now, it’s somewhat limited in what it can capture.
  • DS: People only put data into public databases when they have to.
  • PB: The publishing industry also has to figure out if and how it should deal with these things (OA, standardization, transparency, etc). How to bring together the efforts of publishing and funding agencies scientists towards this end? We should start having DOIs and PubMed IDs to things that are a little less than traditional. It has the potential to push forward science in incredible ways.
  • AA: You donate your sequence data to the public because you get homology out of it. So, scientists are OK about donating data but it’s not alwasy obvious to the researcher all of the benefits.
  • PB: Very few people sit and look through an entire journal anymore: they go to specific papers.  So, you should be able to navigate between papers, abstracts and other components of the paper.
  • DS: Scanning abstracts first, and then drill down as necessary either to paper or supplementary material (or more).
  • AA: supplementary markup is a huge onus on whoever does it. Markup would only be useful if it is in a common format.
  • DS: Many people who expose data satisfy the letter of the law (expose the data) but not the spirit (someone don’t make the best bits available) (Allyson: I’m paraphrasing here as I didn’t catch it all. I may not have this bit correct.)
  • Question: Her hospital is about to give her some clinical data – before that happens, she has an opportunity to say what the best sort of data is. What should be included to make it the most useful?
    • DS: Veterans’ Association (useful taking orders from the top) got it right. A working group that starts with the VA standards and then goes from there might be a good thing.

Allysons thoughts (summarized from the earlier talks): what about standardization efforts for format/syntax/scope? CARMEN? MIBBI-like efforts: is the checklist effort part of MIBBI? And, to all panelists, rather than making your own simulation format, why not use FuGE, which can be used to describe ANY experimental metadata if you want it to, either wet lab or in silico? Tried to ask this, but ran out of time 🙂

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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