Skip to main content

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index] [List Home]
[stem-dev] Notes from today's STEM community callSTEM Community Call September 4, 2014

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
    • 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


Back to the top