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

["Judy Douglas" <judyvdouglas@xxxxxxxxxxx>]

STEM Community Call August 30, 2012

On Call: Jamie, Stefan, Matt, Dan, Matthias, Chris, Alex, Alifya, Kamesh, Judy

 

1. 1.4.0 Release Plan  (tentative 9/25/2012)                      
   Bug Fixes from 1.3.1
   Performance improvements
   Simplified creation of new Disease and Population models (Tools for generating new disease plug ins), AKA model generator

Matt: Involves lots of new code, draft in place,   
   Pajek-file Importer:  
   Enable import of discrete transportation events
   Enable integration between user graphs and existing STEM graphs
   New MapView to visualize the discrete transportation events and the ability to display multiple views of the same simulation
   Polio Example
   Stochastic Modeling Framework
   Ability to Delete Items inside a Graph from Designer Perspective
   Deep copy drag and drop for models
   Refactor
   Create new mixing edges
   Improved UI for decorators view
   New Implementation of STEM Preferences
   NEW * Time adaptive external data source models: IN PROGRESS
   NEW ** Features to simplify new model creation (needs a name): A MAJOR FEATURE

                Matt: Will be available for tryout the end of this week; hides complexities but still need algorithm

 

TO DO PRIOR TO RELEASE:

   A MAJOR RELEASE

  Presentation slides (Jamie and Stefan)

   Check w/ Eclipse IT team; get approval for Danny’s new code

   Code freeze—tentative date 9/14; can push out if necessary 

         
2. New Documentation for 1.4.0
* Wiki practice
* Mixing edges and mixing edge graph generator (DONE) integrated in transportation models page (DONE). Posted on newsgroup
    * map view features    
    * Pajak import tutorial (DONE)
* Best Practice for Developers, writing performance critical components in STEM (DONE)

       Jamie to Kamesh: PLEASE REVIEW, MAKE CHANGES OR SEND COMMENTS TO JAMIE & JUDY
* Additional doc for more realistic food scenario (DONE)
* Better top level food modeling doc (draft created)
 TO DO BY 8/14

**New features/preferences to simplify new model creation (Dan)

3. BfR Summer Institute

Matthias: Great time, hard core agenda, very fruitful, should repeat

Jamie: Perhaps Hawaii next time if India colleagues to attend

TO DO: Matthias will post notes on items next to be addressed

TO DO: Generalize pork production from BfR for potential use elsewhere    

4. ISVEE: International conference on veterinary diseases

EXAMPLE: Mycobacterium Avium subsp Paratuberculosis (MAP), causes Johne’s (prn. Yonnie’s) disease in milk, trans by feces and tit, moves cross species between ruminants, survives pasteurization; suspected causative agent in Crohn’s disease

         Jamie: Met scientist who is from San Diego Zoo, has 20 years data on this; may join in call in future
OTHER HOT TOPICS (incomplete listing)

* Infectious Salmon Anemia Virus (ISAV)
         Isavirus in Orthomyxovirida - one single removal mutation from Avian Influenza; co-infection with sea lice
* Blue Tongue
* H5N1
* Salmonella
* Bovine Tuberdulosis
* Porcine reproductive and respiratory syndrome virus (PRRSV)  - live versus inactive vaccines!!
* Foot and Mouth Disease
* Vectors (Tsetse flies etc), vector diseases...
* West Nile
* Rift Valley Fever

5. Food production: No updates

 

6. Dengue Fever

Kamesh: In Singapore last week; dengue cycle 7-8 years; 1 & 2 dominant strains, 3& 4 less so; no serotype info available, but have incidence data; working to create new models using Singapore data, will discuss further; Singapore colleagues are open to using model for policy decisions if calibrated properly 

TO DO: Kamesh to set up call w/ Jamie to discuss dengue only

 

7. Bugs of the week
Location picker bug when only admin level 2 regions are available: FIXED

Chris: When using German, wants language setting saved somewhere

       Jamie: Need to track, post discussion to facilitate using STEM w/ other native languages

       TO DO: Jamie & Matt will decide how to move discussion/solution forward

8. ITEMS FROM PARTICIPANTS

Matt: Will commit model generation code tomorrow, will publish new version

Danny: Eliminated deprecated classes; has committed changes on preferences

Judy: Requested that team members adding doc send her links so she can review

Matthias: Had conference call w/ USDA scientist today, Dr. Jamah (sp?), whose focus is on predictive microbiology

      Jamie: Has talk on STEM capabilities scheduled w/ Dr. J on September 5 

Chris: Working w/ Danny; has all data zipcode related; Danny will have all finished by end of next week

      Jamie: Will be in code but not 1.4 plan; needs to be committed to Eclipse repository so BfR can use it