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[stem-dev] Corrected notes from STEM Community Call of June 19

Most importantly, please note that the name of the group that is considering using STEM is SAP, not SAT.

Apologies to all.



STEM Community Call June 19, 2014

Corrected version


On Call: Jamie, Stefan, Kun, Matthias, Chris, Judy


1A.  STEM 2.0.2 is up (Thank you, Stefan!!)

==== New Campylobacter scenario

==== Mostly bug fixes

==== Updated Dengue scenario, model


1B. Next release scheduled for October 22


2.  Feature request from Nereyda (restricting air travel for certain compartments, i.e., whether traveler is sick)

==== No update as of now


3. July 3!! Scheduled publication of work on foodborne disease in PLoS Computational Biology


4. Bug(s)

==== None reported

==== Reminder from Stefan for all: Test new release and report back 


5. Items/issues of interest from participants

Jamie: Had call on Tuesday w/ a group (SAP) that is considering using STEM for a course to model malaria; no decision yet; Jamie stated their contributions would be welcome, and that support would be available via stem-dev & the wiki

Chris (Item 1): Standard biology markup language (SBML) System uses compartments, differential equations like STEM, has 200+ tools; possibly do something w/ STEM?

==== Matthias: SBML is a really powerful standard but not for simulations; wants an output model/exchange format/extension that fits to the epidemiological use case to speed up risk analysis

==== Jamie & Stefan: A great idea

==== Jamie: Mapping from one XML to another is not difficult, but some of STEM is very specific to Eclipse; time of Almaden team is limited (Matt Davis is on a project in Australia; Almaden is working with UC Davis on genomics project)

==== Matthias: First put disease model equations (w/o data) as in dengue paper in J Theoretlcal Biol into SBML

==== Jamie: Equations in STEM have been hidden in Java class; w/ new model generator & its graphical editor, may be able to generate equations in XML; would like to see an example

==== Chris: May be able to do this; may post on user group, stem-dev later


Chris  (Item 2): Differential equations from microbiology domain use Levenberg-Marquardt algorithm, not Nelder-Mead as in STEM 

==== Jamie: Could perhaps plug in another estimator

==== Chris: May try


6.  Date for next call set by consensus: Thursday, July 31

==== Judy to put date as item on Newsgroup, advise those interested to contact her; will post item after the July 4th weekend



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