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[stem-dev] Notes from the STEM Community Call on July 20, 2017

Notes from the STEM Community Call on July 20, 2017

On the call: Jamie, Stefan, Nereyda, Taras, Emily, and Judy


NEXT CALL: Thursday, August 10, at 9 am Pacific Time


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

Delayed until later in the year; workaround currently available at


2. Updates

Stefan: Hid the random seed and the stochastic true/false option in the e-core of the disease model; changes made but not committed

Taras: Resolved issue with trigger in mixing rate, not a bug; will let Jamie know if anything here is appropriate for a wiki “fix page” posting

Taras: Finished master’s thesis, to make final presentation; after that, will make public, provide link for wiki, also possibly link for a few days on

Taras: Big workshop on food safety last week at BfR; representative from the Hungarian Institute on Food Safety (where Tekla is) in attendance

Nereyda: Now on 2nd draft of paper based on dissertation, has Judy’s edits

Nereyda: Put edited screenshots into pdf for review, will finalize for YouTube; TO DO: Judy to look over; Jamie to create new wiki category STEM Tutorials on YouTube; Judy to post link to Nereyda’s file as first one

Emily: Jamie and Tekla diagnosed problems importing large Pajek files—files were too big; 74K nodes. Discussion continues in item 3 below


3. Discussion of Emily’s project

Jamie: To resolve size issue, go to stem.ini file, increase heap size to 1 gig; up to half the memory on the machine; per Taras, info is on wiki. TO DO (Jamie?): Copy installation guide, put on wiki

Jamie: Do test, run model; go to preferences on stem; check simulation management, uncheck pause after each; check solver, concurrent worker threads, set number less than 1 of the core and spread across multiple processors; use a smaller graph for testing

Taras: Doesn’t have as many nodes but lots of parameters; TO DO (Taras): Set up call with Emily, Tekla, others who want to discuss; send notice to Judy to post invitation on stem-dev  

Emily: Re post of 19 May on [stem-dev] Rate to probability, deterministic to stochastic; wants to change solver, move those in the susceptible compartment into a protected compartment for 60 days, and then move them back out; issues re (1) noise level and (2) rate; is using trigger on time (deterministic)

Jamie: Use one-direction edge with rate of 1 on protected compartment, then disable; when added noise goes throughout

Taras: TO DO: Send Emily screen shot, etc. of extended model



TO DO: Jamie to email Matthias


5. Bugs

[See item 2, Taras]: Trigger in mixing rate not a bug

515648: Mixing edges when migrating to another polygon; TO DO: Jamie/Stefan to mark closed  


513636: Create option to log internal parameters over time. Workaround: Create a custom compartment

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


6. New contributions on the STEM Wiki, Newsgroup

Nereyda: Will add links as in item 2 above; also to dissertation, podcast, article mentioning her doctoral work 

Taras: Food Risk Labs-Website now includes Matthias’ presentations, now available at 


7. Items from Participants

Taras: Has completed his STEM project

Emily: Is considering attending the Epidemics conference in Barcelona




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