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Re: [stem-dev] Notes from the STEM Community Call on June 8

Hi all,

I noticed that in the notes Tekla had been having issues with the libre office macros. She wasn't able to get it to work with a large number of nodes.

I'm away for a week but when I get back I'm happy to help if there's any issues as I've managed to use the macro with 70,000 nodes. 

I thought it would be good for the STEM community to know that this is possible and for Tekla to know she can contact me next week if she's still having issues (I don't know her email address). 

Best wishes,


On Thursday, 8 June 2017, Judy Douglas <judyvdouglas@xxxxxxxxxxx> wrote:

Notes from the STEM Community Call on June 8, 2017

On the call: Jamie, Stefan, Taras, Nereyda, Tekla, Judy

Next call: Thursday, July 13. Stefan will moderate


*Welcome to Engelhardt Tekla, PhD, Risk Assessor, National Food Safety Agency (Nebih), Budapest, Hungary. New at the agency, now using STEM and studying swine fever

*Congratulations to Nereyda Savilla on the completion of her doctoral studies


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. User queries

TO DO Stefan: Hide the random seed and the stochastic true/false option in the e-core of the disease model. Not a bug; there for backward compatibility

Taras: Trigger doesn’t work in mixing rate and model builder

TO DO: Will post bug; also will email project to Jamie and Stefan to view

Tekla: Queries raised in email of June 6 re Pajek and Libre Office resolved

                Taras: Other option is to use shape file or other software (e.g., Artgis)


3. New server for STEM

Stefan: Need to move the server by the end of the year

Jamie: STEM no longer a primary project at IBM; focus is now food safety

TO DO All: Brainstorm at next meeting


4. Bugs

[NEW BUG]: Taras to post problem with trigger in mixing rate and model builder (see above)


515648: Mixing edges when migrating to another polygon 

513636: Create option to log internal parameters over time 

                Workaround: Create a custom compartment. TO DO: Post on wiki 

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 coming soon to the STEM Wiki, Newsgroup

*Nereyda will share screen shots she developed to help new STEM user; link to her dissertation, podcast, article mentioning her doctoral work 

*Taras will post Matthias’s presentations from the BfR training class


6. Items from Participants

*Nereyda: Will transition dissertation to article; Judy to assist 

*Taras: Discovered minor hack to links on wiki 2012 publications 4 and 5; Judy to locate on Google Scholar and correct



Emily Nixon
PhD Student


School of Biological Sciences
University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Tel +44 (0)117 394 1389

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