DataOne Research Meeting 2: 05/25/2011

• BL: We should not just focus on Kepler, Taverna, but also other programs
• BM: Interests: 
  • the what, how, and why of tools for scientists, and how we can develop tools. 
  • For instance, ecological niche modelling - lots of QA/QC, just to do a single experiment, and it would be nice to understand how complex these are in order to develop them further. 
  • Would like to analyse workflows by: 
    • Data Input
    • QA/QC steps
    • external models
    • iterative loops
    • recursion
    • subject matter (bioinformatics? ecology?)
• Karthik - Experienced with models in R. 
  • Would like to develop a laundry list of workflow dimensions, to find weak points across systems. 
• BL: So, we’re going to look at the workflows out there (such as those on myExperiment). If so, we have to focus on a few aspects:
  • Users: 
    • What kind of users?
    • What are they trying to do?
    • Do they need hand-holding? How accessible are the systems?
    • Do they include R, or other external programs? How do they do this?
    • Are they using the same workflows, or constantly reinventing the wheel?
  • Workflows:
    • plumbing - data management, not the actual science workflows
    • use of shims
    • similar workflows, like the niche modelling types
    • Are the ones which do the ‘real’  work different from the others?
    • Is it 1-of-a-kind?
    • software development (those in production mode at the moment)
  • Depository systems:
    • Kepler Depository has some example ones, especially in packages, which could be mined
    • Find more examples
    • library of the Kepler project, which has a limited user interface
    • myExperiment is still the largest. 
    • BL: “people might not want to share their workflows”
    • Useful in identifying users: would be worth
      • working with them directly
      • using the kepler mailing list (and others) to contact people
      • Some groups in Camera in San Diego, Davis which have in-house Workflows that we could ask for
• Documentation: myExperiment, Kepler site training
  • Develop list of criteria (some above.) 
  • BM has access to 1-2 page description of six work flows, and a summary article on workflow usage.
  • Brainstorming workflow usage
  • (Email the fellow interns with a status update, as per the mentor plan)
  • Heather is making a lab notebook (wordpress)
  • Make three excel sheets: 
    • Users
    • Workflow languages (share with Karthik)
    • workflows themselves
  • Do the relevant reading loaded onto Mendeley
• BL: What’s out there? What is the state of the art? R-scripts? Shell scripts? (Vistrails?)
  • workflows without calling them? is that too out of scope? What’s the outcome predicted for this project?
• BM: Don’t want to start too broadly. Non-published work - how usable is that?
• KR: Identify weak points - some are better, waht gaps are there, examples of non-working ones might be relevant findings?
• Richard leads analysis:
  • randomly chosen subset?
  • x amount of environmental ones, as well (not just bioinformatics)
    • This will be covered more in another call
  • what ones are used (how complex they are)
  • What would analysis entail?
• Karthik : 
  • draft outline for short synthesis paper?
  • higher levels, strengths + weaknesses of programs (…and then suggestions)
    • goal of use, amount of use...
  • Note: ‘less formal ones’, two weeks ago in U Tenn at Nimbus - workflow systems in R - can these be gotten?
  • useful direction to take for next meeting
• Taverna papers - BL’s friend, PhD student (Pãolo?) measurable complexity? Could join us?
  • complement the conceptual analysis
• BL: Provenance repository internship going on as well - on avergage, 30% of workflows are shims. 
  • subsetting, translation, transformation - useful infromation.
• Ultimately, it would be useful to have an annoted bibliography. (Mendeley?)
• Write up synopsis for communications to the public
• Make a public drop-box folder
• Email out to everyone the hours for next week (16:00 GMT/ 11:00 EST, 31-05-2011)
• Fill out the mentor program for the next two weeks
• 29th-30th in UC Davis (Buy Flights - 28th evening). 
• End of call.