Mr. Keil Werner - Stem demo camp

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Mr. Keil Werner - Stem demo camp

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

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