| [stem-dev] Notes from the STEM call on November 3, 2016 |
Notes from the STEM Community Call, November 3, 2016 On the call: James Kaufman, Stefan Edlund, Kun Hu, Matthias Filter, Emily Nixon, Judy Douglas The next call will be in early December; date to be announced Introductions: Emily Nixon, PhD student at the University of Bristol in the UK, doing mathematical modeling of disease in sheep 1. STEM Integration Build is up, stable *Stefan: Will do formal Milestone with Eclipse in the next few weeks *Date for new version: Deferred until ready to do new feature work 2. Ongoing Feature Work, no updates *Nereyda (not on call): Using STEM to model pandemics in biodefense 3. Updates: Kun *Primary concern of Santa Clara public health officials is TB (hard to model) *Interest in Zika in Brazil, Southeast Asia *Will meet with Singapore Minister of Health in December (100s of reported; multiply by 5 since only 1 in 5 symptomatic) *Will work with 6 IBMers in Panama on collecting info in real time using mobile devices, on the street interviews (in one of 5 projects selected by IBM) *Philippine team’s work on model on hookworm infection appears to be proceeding without difficulty *Sent Werner slides for his presentation at Eclipse Europe 4. Other Work: Jamie *Roslyn (Australia IBM) worked with Taiwan CDC, taught STEM and new dengue model using interventions (another one of the 5 projects) 5. Bugs: None 6. Discussion MODELING *Emily: In looking at disease in sheep on neighboring farms, did a lattice; didn’t fit with map coordinates for UK; slow work. A quicker way? *Jamie: Perhaps a square lattice; Chris Thoens did something like this; asks Emily to place a feature request on stem-dev requesting a lattice graph inside a polygon; advises phase has to be right *Emily: How to define county to county spread? *Jamie: Typically model at highest resolution, use containment nodes, perhaps aggregate farms *Stefan: Use migration edges between farms, connect up to a central node *Emily: Some farms use common grazing *Jamie: Flatten model; don’t use admin zones; label farms, roll up results, then do cross county *Jamie: Ability to re-export a graph back to Pajet a feature request; Emily can stay with spreadsheet PROFESSIONAL CONFERENCES *Emily: Any especially helpful? *Jamie: Epidemics (USA-based); International Society for Veterinary Epidemiology and Economics (ISDEE) in 2018 in Bangkok POSSIBLE HACKATHON AT BfR *Matthias: Has master’s student, invites Emily to BfR; will look at Chris’ salmonella model; will communicate with Emily via email STEM USER INTERFACE *Matthias: Took his master’s student 14 days to get STEM running (Java issues) *Jamie: No internal funding for STEM, but committed to open source project; asks Matthias to articulate what he’d like *Matthias: At IBM’s 5 selected projects, create additional videos on using STEM *Jamie: Matthias’ student could make a You Tube video about his problems; IBM team could highlight, put on wiki; need to leverage the open source community 7. Items from Participants *Stefan: After 10 years, will be putting STEM build on a new server, will run faster *Emily: How to update? Jamie: Doc on wiki; don’t need to update every week; do NOT delete old version; all your work is there; currently a Windows problem with updates, will help Emily with this *Judy: Lancet piece on potential Zika threat in Pakistan; Kun commented it seems on target |