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[stem-dev] Notes from the STEM community call November 6, 2014

STEM Community Call November 6, 2014

On Call: Jamie, Stefan, Kun, Nereyda, Judy

Next Call: Thursday, December 4, 2014


1. STEM 2.0.2 up

  • Next release delayed to January 9, 2015 to allow for new plug in to measure poverty (paper on Ebola used measures of lighting in 3 towns as a measure of GDP)
  • Integration builds will continue to appear every Friday


2. Feature Requests

  • Restricting air travel for certain compartments
    • Nereyda: Working on model; found air travel in wiki; at adviser’s request, is changing her proposal from smallpox to possibly pneumonic plague; feature request still stands
    • Jamie: Could she consider working on ebola with the Almaden or Australia teams?
  • Implement roads in Africa
    • Jamie: Cancelling to focus on new plug in 
  • New plug in to measure poverty
    • Jamie:  See item 1 above


3.  Items from BfR: Deferred for update when Chris (BfR) is on the call

  • Possible use of the standards-based Systems Biology Markup Language (SBML) for predictive biological modeling
  • Possible use of Levenberg-Marquardt algorithm Chris


4. Bugs

·         Zero population region in Africa: FIXED, have 6


5. Items from participants

  • Judy: Will use Jamie’s statement to respond to query re paper  
  • Stefan: Eclipse is deleting everything in old repository on SDN prior to move to GIT
    • Jamie: Need to check?
    • Stefan: Thinks Matt migrated the history
  • Kun: In modeling ebola, no enough data, problem with accuracy of case reporting; trying to calibrate, using sensitivity; can we change the sequencer?
    • Stefan: Could be a big feature
    • Discussion defined three new feature requests listed below; Jamie to do  the second; Stefan (?) the first and third


Three New Feature Requests to allow modeler to

      • Have batch to control sequencer
      • Log automated experiments
      • Modify sequencer to get automatic experiment to run batch


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