Mr. Keil Werner - Stem demo camp
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  • 1. STEM:The Spatiotemporal Epidemiological ModelerOpen Source Disease Modeling Application Available Through
    http://www.eclipse.org/stem/
    IBM Almaden Research
    IBM Haifa Research
  • 2. 2
    Introduction
    General Information About STEM
    Analysis of Seasonal Influenza Data from ICDC and Maccabi Health
    Simulations based on Seasonal Flu Data
    Swine Flu
    Public Health Information Affinity Domain and Collaboration with MECIDS
  • 3. 3
    STEM is Open Source
    http://www.eclipse.org/stem/downloads.php
  • 4. 4
    STEM is a Framework
    Epidemiological Compartment Models
    Standard SEIR model
    Standard SIR model
    Births
    Births
    S
    E
    I
    R
    S
    I
    R
    Deaths
    Deaths
    S: susceptible
    E: exposed but not yet infectious
    I: infectious
    R: recovered
  • 5. 5
    Human Flu
    Swine Flu
    “Mixing Cell
    The Many Vectors of Infectious Disease
  • 6. 6
    US Counties (3109) Edges
    Common
    Border Edges
    Interstate Highway Edges
    Air Travel Edges
  • 7. 7
    STEM Core Integration Engine
    Choice Between
    Finite Difference Solver (fast, good for demos)
    Runge-Kutta-Fehlberg (RKF45) adaptive integration
    Adaptive step size
    Very efficient
    Synchronized across threads (multi-core engine)
    Accurate
    Computational error is estimated and controlled and an appropriate step size set automatically
    User Contributed Solvers
  • 8. 8
    Goal: Evaluation of Public Health Policies
    Masks
    No Air travel
    HCN/HL7
    Vaccinate
    Weather
    Air Traffic
    Masks/No Air
    Multiple parallel scenarios identically initialized from current real world conditions and simulate each simultaneously forward in time.
    ?
  • 9. 9
    MECIDS
    iCDC
    France
    (Government, Universities)
    Northrop
    Grumman
    Why Open Source?Need for an International Community
    Eclipse Foundation
    UPMC
    Pitt
    Stanford
    MIT
    University of Vermont (UVM)
    U. Helsinki
    In discussion/meetings planned
    University
    of Edinburgh
    UC Davis
  • 10. 10
    Demo
  • 11. 11
    Simulations Based on ICDC Influenza Dataas initial condition
  • 12. 12
    Recent H1N1 Outbreak
  • 13. 13
    What are the parameters for the recent H1N1 outbreak
    What is Ro?
    Case report data not complete
    What could we learn from public data
    When first cases (~10) showed up in NY there were thousands in Mexico city
    Flu in Mexico peaked shortly after spread to air transport system
    Can we use the spread by air transport as an indicator for Ro ?
  • 14. 14
    How Many Cases had developed in Mexico when Flu first appears in NY ?
    County/State
    National
  • 15. 15
    Time to epidemic peak [days after I(NY)>~10]
  • 16. 16
    Example Social Distancing Scenario
    • Delay in Flu with Temporary Social Distancing
    • 17. Model does not include seasonal forcing