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