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[stem-dev] STEM Community Call for June

The June Community Call for the STEM will take place this Thursday, June 8, at 9 am Pacific time. As always, we welcome all members of the research and public health communities to join in the call, to learn more about STEM as an open source tool. If you are interested in participating, please contact me, judyvdouglas@xxxxxxxxxxx, for call in information. The agenda for call appears below.


Agenda for the STEM Community Call on June 8, 2017


1. STEM 3.0.0 Milestone 5: Release to follow solution of problem with launcher on Mac

A major task, making the build compatible with Eclipse and awaits resources (summer intern? post doc?)   Currently a workaround is available at


2. Issues Raised/Resolved

Problem setting the seed on the stochastic solver and using the nonlinearity coefficient resolved, emails posted on stem-dev 97(6) 11 May

The random seed and the stochastic true/false option in the e-core of the disease model do not work in the current version but can’t be removed without breaking the build and are thus to be hidden (Stefan?)

Workaround tested?

Resolution of problems with predicates posted on stem-dev 97(7) 11 May

Taras’ response to paper using deterministic model

            Received line of code where noise is computed from Jamie; see stem-dev 97(6) 11 May

Issues with birth and death rates posted as bugs 513636 and 515654 (see below)


4. Bugs: All the bugs listed require major development efforts; thus all are Feature Requests; addressing them awaits resources

515648: Mixing edges when migrating to another polygon 

513636: Create option to log internal parameters over time 

515654: Calculating disease model with model generator; multiple aging populations

[Bug on stem-dev]: Rate to probability, deterministic to stochastic

Workaround: (1) Hack it using math.rand from java math to add noise to the infection process and add  new hidden compartment in susceptible line code.  (2) Try with finite difference solver and jiggle the “f” value. (3) Go to the model creator on wiki and use the _expression_ editor to create a transition, “f”=random (0-1). Emily to test, write up for other users


5. New Contributions Available to STEM Users

Links to new resources posted on stem-dev and the STEM Newsgroup now appear on the STEM Wiki (Koch Institute lecture series, BfR course material, Taras on epi modeling)


6. Items from Participants



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