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[stem-dev] Notes from the June STEM community call

STEM Community Call June 19, 2014


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 schedule 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 (SAT) 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 another project, Almaden working UC Davis on genomic pathways)

==== 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