STEM Community Call September 4, 2014
On Call: Jamie, Stefan, Kun, Chris, Judy
1. STEM 2.0.2 up; next release scheduled for October 22
2. Feature request re restricting air travel for certain compartments
- Nereyda: Working on model. See more under item 6
- NEW FEATURE REQUEST
- TO DO (Jamie) : Implement roads in Africa. May be able to get from open street maps
3. Possible use of the standards-based Systems Biology Markup Language (SBML) for predictive biological modeling
- Chris: Uploaded example file; not very intuitive; used SBML, modeled SIR as species (not compartments) in simple model
- TO DO: Carry item forward
4. Possible use of Levenberg-Marquardt algorithm
- Chris: Has yet to explore
- TO DO: Carry item forward
5. Bugs
· Some code cut in model generator: Status: FIXED
· Zero population region in Africa: FIXED, no longer throws exception
o TO DO: Log a warning to alert user
o TO DO: Check world for zero population areas
6. Items from participants
- Kun: Working on ebola model for publication. 8-compartment model for 3 countries, unique in that transmission continues after death, also in that recovered individuals can transmit by sexual contact; developing proposal
- Jamie: How best to share in spirit of open source? When to put something up prior to publication?
- Stefan: Issues re mixing parameters if extended to all of Africa, also transportation model
- TO DO: All discuss further off line
- Nereyda: Wants to visit Almaden before end of year (Monday or Friday preferably) to validate her work, enhance skills
- TO DO: Will implement model and share before visit for review by Almaden team
