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[stem-dev] Notes from today's STEM community call

STEM Community Call December 4, 2014

On call: Jamie, Stefan, Chris, Kun, Nereyda, Judy

Next call: Thursday, January 8, 2015


1. STEM 2.0.2 up

  • Next release delayed to January 9, 2015
  • Bug fix for regression in latest dengue model available in weekly integration build
    • Will be part of 2.0.3 in January
    • Judy to post on newsgroup
  • Dengue model being used by Kamesh, IBM India, in work for Singapore
    • Possible talk on Ebola call by Kamesh on using STEM for this?
  • Work with info from satellites on lighting at night showed ineffective as a measure of poverty in three villages (Ebola); no simple correlation
    • Jamie will explore using statistics on hospitals and clinics as an alternative
  • Integration builds will continue to appear every Friday; they are up to date


2. Feature Requests

  • New plug in to measure poverty: Jamie is exploring stats as in item 1 above
  • New plug in for roads in Africa: Jamie still working on this
  • Restricting air travel for certain compartments: Nereyda moving from smallpox to pneumonic plague; nothing new to report
  • Three  new requests to allow modeler to: work on this yet to be done
    • Have batch to control sequencer
    • Log automated experiments
    • Modify sequencer to get automatic experiments to run batch


3.1. Update on Ebola Modeling: Kun

  • Weekly call very successful
  • Have open sourced Ebola model on transmission (funeral, sexual transmission after recovery)
  • Working with University of Melbourne on importation
  • Working with Richard Stovkis, Chief Medical Officer at Cures United on modeling interventions
    • Will have 120 healthcare workers in Sierra Leone in January 2015
    • Will have mobile lab center, 90 minutes from test to result
  • Details, including slides, available at


3.2. Update on Ebola Modeling: Jamie

  • Kun invited to participate in White House conference call
  • Simone invited to two events in DC, first by Intel, second by House of Representatives 


4. Items from BfR: Chris 

  • No report re Systems Biology Markup Language (SBML) or Levenberg-Marquardt algorithm
  • Will look at one software tool for biology and epidemiology 5. Bugs: Any to report?


5. Bugs: See item 1, fixed


6. Items from Participants

  • Kun and Stefan to present to Science Working Group at EclipseCon in March
  • Update from Matt: working with University of Melbourne and Australian government on Ebola in effort to build a more accurate, point-to-point air travel model (purchased data), bidirectional migration; hope to have report on progress soon
  • Chris attended meeting in Berlin, heard researchers from a German university present their work to build methods to model numbers of mosquitoes in certain areas and the likelihood that they carried certain diseases
    • Chris to email them regarding possible collaboration, contribution of their model
  • Jamie invited to annual conference on neglected tropical diseases to be held at London Zoo in March
    • Kun may be in Spain to present in March, if so, could attend
    • Chris might possibly join Kun there


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