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

STEM Community Call October 13, 2011

On call: Jamie, Eric, Matt, Stefan, Kun, Werner, Judy

Release planning
Reminder: Will release STEM 1.2.3 on Nov 21 (RC1 Nov 1); need to delete old property files for translation (have moved to Babel): Matt will do; Spanish will also be added

Reminder: Target date for 1.3 is still (1/07/2012), will include the items below

* Ten years of Earth Science Data (2000-2010) available as STEM ''Features''
* Malaria Disease Model (''Anopheles'' calibrated)
* Dengue Fever Disease Model (''Aedes'' not yet calibrated)
* Additional NLS + User ability to switch languages
* Logger Framework with new loggers
====Release new loggers for 1.2.3
====Delete old loggers and views for 1.3 Will involve a little overlap
* Shape File Import Utility. Will discuss with Matthias. (Dependency on Open Map CQ). Matt will re-open
* Integrating external models for study of food based transmission
* New Differential Equation solver(s) from commons.math library
* Bug Fixes from 1.2.2
*** Need presentation slides for 1.3

New doc needed for 1.3

Status: No additional updates
*  Dengue
*  Initializers
*  Loggers
*  Malaria (done)
*  Mosquitos VCAP (done)
*  Shape file importer (NEW)
*  Solvers
Bug of the week. Bug 353939 Project Explorer seems to be broken when STEM workspace path contains a space. Resolution: This is not a STEM bug (hence close it) but an Eclipse requirement. Jamie/Judy to update documentation for developers and startup

Items for Newsgroup this week
Item on new framework for error handling and messages
. Stefan has posted
Item on new loggers. Matt will post       
Update on Dengue model status
 JK implemented Newton-Raphson to solve couples nonlinear equations (matlab class) to test/confirm steady state solutions for full model. No discrepancy, need to find bifurcation point, Jamie, Kun to talk; Jamie has sent Kun link to mathlab. Tom Waraporn has sent dengue fever and malaria data from Thailand                           
New Malaria mapping algorithm
Status: Moving forward, will input into paper       
STEM NLS language packs are up on Babel
Status: Will send note when all is done & all are ready. Jamie will do
Todo: (1) Delete Migrated files from SVN; (2) New Property Files from Stefan, must update Babel for 1.2.3 release (on website)
Ideas for future STEM demos
>FD vs Integration
>Data Import example (playback)
>Data input example (initialize from csv)
>Data logging image and data examples
>Dengue Fever example(s)
> what else? No urgency, can do in January
>>> Can we do a YouTube on each one ? Stefan, what did you use to do the screen captures?

>>> Need to plan code freeze November 1st so we have 1 month to build and test scenarios for workshop
Report from Stefan on New Error handling
Four issues/questions raised re disease models, population models, error messages, & cloning. 
 First issue: When a disease model is initialized (creating and initializing the disease model label and label values needed to keep track of the dynamically changing state of the disease), it depends on having a population model (of the same population identifier) with its label/label values already initialized beforehand. If it cannot find one, it automatically generates an instance of a StandardPopulationModel with zero background birth/death rate. Proposal: Get rid of the automatic population model and add error/warning message; will do for release 1.3.0 Vote taken, proposal passed.

Stefan will write note to
Remaining issues Jamie, group: Leave these items for further discussion
ii) Right now, population models must be located beneath the disease model in the model hierarchy. The only real reason why they can't be at the same level is that for Standard Population Models (with fixed background birth/death rate), the population numbers are adjusted to correspond to the starting date of the sequencer. So if the population data is valid 2006, and the sequencer starts in 2011, the numbers are  advanced five years given the background birth/death rate. The disease model must be aware of this when it is initialized so it must be above the population model. Again, the question is whether this is confusing the users more than helping them. Also, since we have many other types of population models that does not change the initial population numbers from the start of the sequencer (e.g. seasonal, mosquito), perhaps we should get rid of this feature altogether.

and iii) If we were to get rid of the feature, perhaps replacing it with an alternative method such as using a  "population re-scaler" is a better option. This has the benefit of working for any type of population model used.
Discussion: STEM design philosophy (portability and reusability of models). Let's get a list of proposals including
the following:
 A. Create new, Population Re-scaler object, specifically to reset population by calendar (should iii come before ii?) Stefan: Re-Scaler seems more straightforward
B. Eliminate the nesting requirement  Stefan: Question is how to re-use
C. Require Nesting but with change A, tolerate parallel placement of populations and disease models
D. ?? other alternatives

iv) discussion on cloning. This would be a huge change.

Items from participants

Eric: Looking at future versions of GEM; very limited model; required to work on pc or laptop, as is, can do aerosol spread; would like ability to predict spread of the disease; need system that is generically applicable, easy to scope and run; needs to be fast.

Jamie: STEM differentiates between initialization and spread, has ability to build model for aerosol spread. Matt: Can run a global model a few seconds/day (depending on what you are logging)

Jamie and Eric: Will talk at upcoming conference both are attending

Regular call next week. Judy will confirm w/ Matthias




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