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

STEM Community Call March 1, 2012

On call: Jamie, Stefan, Matt, Kun, Matthias, Chris, Alex, Judy


1. 1.3.1 PLAN
Plan still available for comment and revision

New Target Platform using Eclipse 3.7.2 and EMF 2.7 is available for download 
All developers can now update their environment

TO DO: Matt will send email; Jamie will post
2. NEW DOC FOR 1.3.1
*New Dengue example

*Possible polio example

*Possible chicken pox example


i) GUI or tool for user-friendly (= no need for coding) disease model implementation

Matthias: Is it possible to include dengue disease model in disease model library for STEM?

Jamie: Doing so involves technical issues—currently a single “toy” model to run out of the box; ant script could do more, but dengue takes a long time to run, cannot run on a laptop; real model, involves public health data that’s not part of STEM

Matthias: Already have a lot of sample models; is it possible to put disease models into a folder for users? Example: Work Alex is doing now; want to create a library of disease models, so could go to literature, search for disease models and integrate them with parameters into STEM library to use in case of an emergency; could put in disease models that have already been published

TO DO in 1.3.1: Include preconfigured disease model examples with parameters; use ones in the sample scenarios; some require a population (e.g. mosquitoes); error message will tell users external data needed

Challenges: Replay mechanism should be able to replay public health surveillance data (non-STEM generated); initializer needs to point to a class or name; need to add in parameters for polio, TB, and (especially) dengue

TO DO: Matt will prepare list of models

Chris: Maintain list, edit ant script

Item will appear on agenda for next week’s call for further discussion 

ii) Sequencers should allow (e.g.) year or month as unit of time

Stefan: Minor problem, working with this


Matt: Reader is now committed; working on different projections (the 4-5 most common ones); currently STEM offers only one projection format

4b. Still waiting on Eclipse re: SHAPE FILE IMPORT/IPZILLA (update)

TO DO: Matt will post comment in IPZILLA, noting that major components have been implemented but more from open map would be helpful, e.g., some GIS stuff; will wait to hear from Eclipse re the CQ 

Matthias: Happy with what we have now


Jamie:  ESRI purchases map of Europe via Michael Bauer; Michael Bauer might allow usage of maps for a limited purpose (a simplified set of polygons, not shape files); GSK Marketing and Research would charge more; UN website has ambiguous license

Matthias: Will find out whether the German agency that provides BfR with maps would contribute the maps of Germany to Eclipse 



Chris on Chicken pox: difficult to find link on wiki, not much there

Jamie: Perhaps look at the effect of vaccination, as in France, where children do not need to be vaccinated to go to school

Matthias: Perhaps Chris can look at this when and if he has free time; resources now are limited

Kun: For polio demo, now have model with 9 compartments that would allow incorporate of complexities (e.g., OPV  reversion)

                Jamie: Lit search showed no published models that capture reversion; have call tomorrow with expert in area


Matthias: Still need a way to make it easier for users to create disease models without downloading STEM; if not a GUI, perhaps an interim solution

Jamie: Perhaps a model with many compartments with a wizard for inputting equations and entering the label name? A simple template tool could do so on demand (without eliminating Java)

TO DO: Matthias will identify two examples he really wants; will put the discussion on the Newsgroup; Jamie will develop proposal(s)  


TO DO: Matthias will send Stefan more information, in addition to that he has already sent



Chris: Added information on pipe transport; will continue on stem-dev

                Jamie: Flag on migration or refactor edge to = label?

                TO DO: Carry item over for discussion on next week’s call 


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