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[stem-dev] Notes from the STEM Community Call on April 7, 2016

Notes from the STEM Community Call on Thursday, April 7, 2016

On the call: Jamie, Kun, Matt, Nereyda, Chris, Werner, Judy


Next Community Call: Thursday, May 12th


1. STEM Milestone build 3.0.2, aka Java 8/Eclipse 4 build

*Up and tested

*Date for 3.0.3 to be scheduled for June (Stefan)

2. Feature requests

*Evolving disease model to address genome. Jamie is working w/ Matt and Kun on this. 

*Extended shape file capabilities using a Pajek file. Chris has completed; is in and documented.

*Progress with travel model. Nereyda and Jamie to work together on April 8, will report in May.


3. Updates

*Zika. Kun is tracking; no decision yet as to how/whether to address.

*Followup on STEM workshop with Roslyn and Raymond. Completed.

*ISCB Fight against Ebola. Decided not to prepare a proposal.  

4. Bugs
*Bug 465981: Kamesh’s problem with dengue model. TO DO: Kun to verify.

*New bug: Running headless. Matt has done workaround. TO DO: Jamie will specify display in FHS window, will test; if it works, will document on wiki; if it doesn’t work, Philippine team will address.

*New bug [#465981?]: Batch experiments failing when transformation decorator is used. Influx of reports on news group from users, perhaps due to use w/ zika; bug real, but not a high priority.


5. Items from participants

*Jamie: Will be writing new papers on evolving disease model this summer w/ UC Davis microbiologists. USDA has genome project identifying 5-6 SNFs in salmonella to use in tracking;  SNFs in bacteria aren’t stable; when a mutation occurs, the genome changes and there is a quasi species. Goal is to combine epidemiology and genomics. Builds on earlier work Chris did w/ transformation decorators for slaughter houses; also Matt’s model generator for discontinuous transformation. Will model cross strain immunity, change in genetic distance. Given food safety focus, is this of interest to BfR? TO DO: Chris will speak with Matthias.

*Jamie: Located multiple papers using STEM on Google. TO DO: Judy will go through, find any not cited on STEM wiki and add to listing there. 

*Chris: Institute in Berlin responsible for infectious diseases in humans has hired a new mathematical modeler, Dirk Baughman, previously at Northeastern U in Boston, where they used another modeler. Baughman finds too many models that too complicated and make it hard to draw conclusions. Jamie: Would like introduction; Kun’s paper on three dengue models deemed one to be over determined; multiple approaches to modeling exist.

*Werner: To attend Eclipse Science Working Group June 10. Jamie: If any Eclipse software engineers interested, could use their help on fixing things that broke when STEM moved from Eclipse 3 to Eclipse 4; interested in WG if we can retain our URL, someone from IBM already involved. Jamie: Reached out to steering committee’s Matthew Goering on Linked In. TO DO: Chris will check with Matthias as to BfR’s interest in a meeting in Berlin, will let Werner know.

*Jamie and Kun: Want to talk with Matthias about projects, US funding opportunity on food safety (paper IBM and BfR co-authored). TO DO: Chris to let Matthias know.



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