STEM Community Call Agenda
 
1. V 2.0 Milestone 2 is now available
V 2.0 Milestone 3 planned for 6/18

Milestone 3:
            Bug Fixes
            New Stochastic model solver
            Visual Editor initial checkin
                    New Measles model
                On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            **Stochastic Modeling - New Solver doc.  After Eclipses release we need to contact eclipse legal re Apache
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated Upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        ==== Added new document Stefan’s new periodic control graph generator
        ==== documentation for MMR model
        ==== Shape file graph generator - need new screenshop on wiki
               
 TO DO (ALL): Please Post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language

3. Stochastic modeling - two new plugins. Update

4. Bug(s) of the week
400920 Update: Do we have doc (updated screenshot) for Shape file graph generator ?
Chris implemented new feature to get area from SHP file import
 
Chris will NOT open a bug- new issue resolving target platform with Eclipse 4 is FIXED

FEATURE Request: Fix aggregate time series view
Feature Request: Directionally biased mixing model (with periodicity in time)
   
7. Items from Participants

STEM Community Call May 16, 2013

On Call: Jamie, Matthias, Chris, Alex, Stefan, Matt, Judy

 
1. V 2.0 Milestone 2 is now available

Milestone 2:
            Bug Fixes
            New Measles model
                On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            Stochastic Modeling - need to watch apach.math.commons library  
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        ==== Added new document Stefan’s new periodic control graph generator
        ==== Documentation for MMR model
        ==== Shape file graph generator - need new screenshop on wiki; Chris working on this (see item 5, bug 400920)

Added item re data: IBM recently purchased zipcode and admin data for Germany for good price from ESRI]

             
 TO DO (ALL): Please post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language

3. H7N9 model status and update
Stochastic modeling in progress...

Stefan working on how best to implement in STEM

4. GIT Transition Completed Successfully!!
Anyone have issues?

5. Bug(s) of the week
400920 Update: Chris will complete, implement area import, do doc (item 2 above), check w/ Alex, and close
 
405549 Closed, Done

Chris had troubles running STEM 2 product;

Fixed this windows XP problem with - console option.

Workaround, we do not add -console

Chris will open a bug- new issue resolving target platform with Eclipse 4

7. Items from Participants

Jamie: Risk map of H7N9 at http://blogs.biomedcentral.com/bmcblog/2013/05/04/mapping-the-risks-of-h7n9-infection-in-china/ raises new possibilities; will create feature request for a directionally biased mixing mode w/ periodicity and time

Matthias: Finalizing biosecurity article, will send out to co-authors tomorrow to look over; need early next week

Stefan: Date for V2 Milestone 3 set for 6/18/2013  

STEM Community Call Agenda
 
1. V 2.0 Milestone 2 is now available

Milestone 2:
            Bug Fixes
            New Measles model
                On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            Stochastic Modeling - need to watch apach.math.commons library  
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated Upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        ==== Added new document Stefan’s new periodic control graph generator
        ==== documentation for MMR model
        ==== Shape file graph generator - need new screenshop on wiki
               
 TO DO (ALL): Please Post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language

3. H7N9 Model status and Update
Stochastic modeling in progress...

4. GIT Transition Completed Successfully!!
Anyone have issues?

5. Bug(s) of the week
400920 Update: Do we have doc (updated screenshot) for Shape file graph generator ?
Should we close this or more to do?
 
405549 Chris: Update on troubles running STEM 2 product; Same issues as before...windows xp, java 6. Two machines - does not have admin rights on either
** Matt: Probably OSGI loader was getting deadlocked due to something the Almaden team was doing behind the scenes

Chris - do you have a new issue with Eclipse 4?
   
7. Items from Participants

STEM Community Call May 9, 2013

On Call: Jamie, Stefan, Matt, Kun, Werner, Judy

Please Note: Agenda items for this week, May 9, will be held for next week, when BfR team members are on call

1. V 2.0 Milestone 1 available Tuesday, April 2 .
Plan for Milestone 2 on May 13^th updated on website; confirmed on track for May 13^th date
Milestone 1:  On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            Stochastic Modeling - need to watch apach.math.commons library  
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated Upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        ==== Added new document Stefan’s new periodic control graph generator
        ==== documentation for MMR model
        ==== Shape file graph generator - need new screenshop on wiki
               
 TO DO (ALL): Please Post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language?

3. H7N9 Model status and Update
Stochastic modeling in progress...

4. GIT transition: Completed Successfully!!
Anyone have issues?

5. Bug(s) of the week
400920 Update: Do we have doc (updated screenshot from Chris) for shape file graph generator?
Should we close this or more to do?

405549 Chris: Update on troubles running STEM 2 product; Same issues as before...windows xp, java 6. Two machines - does not have admin rights on either
** Matt: Probably OCI loader was getting deadlocked due to something the Almaden team was doing behind the scenes

6. Werner: Rare-disease diagnosing search engine, also big data

At meetings, made contacts, including w/ Danes

Shared info via email, newsgroup
   
8. Items from Participants

Jamie: Stefan has contacted a potential new contributor to STEM

The Almaden team has visitors this week, so the call will be short.

It will address the Git Migration only.

Expectations are that the migration to Git will be done by this Wednesday, so the call will just be to confirm that no one had problems.

Everyone is asked to check STEM DEV for updates on GIT and to send a note to STEM_DEV if any problems arise.

Thanks to all.

STEM Community Call April 25, 2013

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

 
1. V 2.0 Milestone 1 available Tuesday, April 2
Plan for Milestone 2 on May 2nd as on website: still on
Milestone 1:  On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            Stochastic Modeling - need to watch apach.math.commons library  
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated Upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        ==== Added new documentation for Stefan’s new periodic control graph generator
        ==== Documentation for MMR model 
        ==== Shape file graph generator - need new screenshot on wiki (Stefan to send to Jamie to put up
               
 TO DO (ALL): Please Post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language

3. H7N9 Model status and Update from China: Jamie

Stefan & Kun have built two models, one bird-to-bird, one bird-to-human

Question: How would human-to-human be different?

Question: How long does it take a chicken to recover from the flu? Alex will ask Yvette

4. Discussion/Description of new measles model: Stefan

Working w/ researchers in Britain, using Chris’s mechanism for an aging population in an SEIR model

Introducing new compartments for (1) newborns w/ maternal immunity and (2) newly vaccinated    individuals who have not yet built up immunities (takes several weeks) 

5. GIT transition plan update
===Chris: Works ok with HTTPS
=== We can proceed when ready
===Update on migration plan when Matt is back

6. Bug(s) of the week
400920 Update: Shape file graph generator is not intuitive
Can now import multiple populations, have made more intuitive; need new screenshot on wiki
405549 Chris: Update on troubles running STEM 2 product; same issues as before...windows xp, java 6. Two machines - does not have admin rights on either
** Matt: Probably OCI loader deadlocked due to something the Almaden team was doing behind the scenes
** Did we respond to user with Uganda Shapefile bug?

** New user in India (Pandit) in India ran ok following query/response, hopes to join call in future

STEM Community Call Agenda


1. V 2.0 Milestone 1 available Tuesday, April 2 .
Plan for Milestone 2 on May 2nd updated on website
Milestone 1:  On Track: UI, model development workflow, builder tools, xtext, all in STEM
                Add model generator Feature to STEM-core (with required plugins)
                Customize Project Explorer (show/hide generated Java code)                            
                                Hot injection of generated plugins
                                 
Future V 2.0 Release Features to include:
        Xtext model generator feature  
        Graphical Model Design (GUI for code generation)
            Bug Fixes from 1.4.1
            Performance improvements
            Advanced Dengue Example
            Stochastic Modeling - need to watch apach.math.commons library  
   
2. New Documentation for 2.0
        ==== Pubs updated on wiki
        ==== Updated Upcoming (and recent) talks on main website
        ==== Use of model generator inside of stem (vs in the dev environment)
        **** Added new document Stefans new periodic control graph generator (Judy, can you please take a look at it?)
               
 TO DO (ALL): Please Post recent/upcoming talks (also publications) on wiki or send to Judy to post  
...we should write a paper on the Compartment Transition Definition Language

3. ****  H7N9 Model status and update with latest news from China

4. Discussion/description of new measles model

5. GIT transition plan update
===Chris entered bug re HTTPS; BfR firewall blocks GIT
===Update on migration Plan if Matt is back

6. Bug(s) of the week
400920 Update: Shape file graph generator is not intuitive
**Need to work on ui for customizing Configuring .shp import (new feature request)
Chris: Update on troubles running STEM 2 product; Same issues as before...windows xp, java 6.
**Matt: Probably OCI loader was getting deadlocked due to something the Almaden team was doing behind the scenes
   
7. Items from Participants