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

STEM Community Call August 7, 2014


On Call: Jamie, Stefan, Kun, Nereyda, Chris, Hussam, Judy


Introductions: Hussam Ghunaim, graduate student at the University of Bridgeport in Connecticut, plans to use STEM in doctoral dissertation



1. STEM 2.0.2 up; next release scheduled for October 22

* Chris: Date okay, not additions/issues

2. Feature request re restricting air travel for certain compartments only

* Nereyda: Will report next month when she has more specific

3. Possible use of the standards-based Systems Biology Markup Language (SBML) for predictive biological modeling

* Chris: Has successfully tried one of the tools available that supports SBML with SRI compartment model; still looking into features

* Discussion: Possible to import SBML file into STEM model builder...or vice versa?

* Chris: Export possibly easier; will attach example of what he has done this far and start discussion thread

4. Use of Levenberg-Marquardt algorithm

* Chris: Still exploring, will report

5. Comments on paper on foodborne disease published in PLoS Computational Biology

* Kun: Reader raised issue whether it is safe to assume that food is consumed where purchased

* Kun: Explained plan to explore further, including possible use of information from supermarket loyalty programs

* Jamie: Having reader comments on published paper is a rewarding experience

6. Bugs

* Stefan: All, please post any bugs on Bugzilla

* Two “bugs” currently posted are actually feature requests

* TO DO: Jamie and/or Stefan will respond to those two bugs

7. Items from participants

*Kun: Has received positive response from Journal of Food Control  on paper requesting revisions, specifically more details so readers can replicate methodology; will work on this next week and resubmit 

* Stefan: Still working on issue re checkout

* Hussam: Finding wiki documentation on STEM hard to follow; some screens outdated

** Jamie: Email pages to stem-dev

** Stefan: If trying to write a disease model, try to use model builder

** Jamie: Go to You Tube video on model builder, download automated example on Nelder-Mead



NEXT CALL: Thursday, September 4, at 9 am Pacific time


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