OpenWetWare:Steering committee/NSF BDI Grant/Outline

Research Plan

Laboratory Information Management

• Individual laboratories and collaborative groups generate many types of information.
  1. Laboratory protocols -- recipes, expected results, tips and tricks
  2. equipment -- operation, calibration, expected results
  3. Current research plans/researchers --
  4. research results
  5. Stocks -- locations/quantities of chemicals, biologicals
  6. Information aggregation -- strains, collections of useful tools
• Ways to access information
  1. protocols
     • current access; methods section of published research, aggregated protocol collecions (CPMB), disparate collections of protocols from lab web pages, unpublished lab protocols & personal communication
     • problems; not detailed enough to enable replication, nature wiki article
  2. equipment
     • current access:company documentation, personal communication
     • company documentation is often insufficient to troubleshoot problems, get ideas on expected results, et cetera. individual expertise within a lab, often departs with individual. no mechanisms for sharing this information between labs other than direct contact.
  3. current information on what's happening in lab
     • individual laboratory websites, publications, personal communication, conferences (posters & talks)
     • often out of date; current information largely unavailable... not all of it due to secrecy (ie., they talk about it at conferences, you just have to be there).
  4. research results
     • peer-reviewed publication
     • often insufficient, not always easy to find information; negative results, smaller results that don't go into paper
  5. stocks
     • internal laboratory documents, LABASE (Chan & Endy, antiquity)
     • historical records lacking,
  6. information aggregation
     • disparate online and offline information
     • could aggregate data to ease access to information; i.e, e. coli genotypes
• Some communities have been able to harness information for tight knit communities. For example C. elegans. This works when community is very centralized; everybody knows each other. Not many communities have the centralization, resources, tech savvy to be able to pull something like that off. In addition, Information must be very structured. Still miss out on other many other sets of data. Not very extendable on the fly.

OpenWetWare

• OpenWetWare was an experiment in trying to see if we could use a wiki to solve some of these problems.
  • A wiki is...
  • OpenWetWare is...
• OpenWetWare, going through above problems