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LSDTM

LSDTM (Location-Specific Disease Transmission Models) is a workflow project that streamlines the process of running location-specific disease transmission models on the Olympus cluster of the Pittsburgh Supercomputing Center 💻

LSDTM Quickstart

  1. Clone or download LSDTM project
  2. Ensure fred/pfred-0.0.8 and fred_populations/spew2synthia-1.2.0 (optionally fred_populations/United_States_2010_ver1 as well) modules are available in working environment (module avail)
  3. Determine the population ID (for example, '2010_ver1_01' is the synthetic population ID for Alabama)
  4. Run [path]/LSDTM/lsdtm.sh [[-p Synthetic Population ID] (OPTIONS: [[-e Ecosystem] [-o Output Directory]])] | [-h Help]

For more information please visit the wiki 📖