Overview

Mission: make SBML simulations great again

The idea of sbmlsim is to provide a simple abstraction layer for running simulations with SBML models in python.

Simplicity

  • make it easy to encode simple simulation experiments with a focus on numerical ODE simulations

Simulation

  • timecourse simulations
  • combined simulation experiments (combination of changes)
  • parameter scans
  • parameter sensitivity analysis

Reproducibility

  • A simplified exchange language based on JSON is part of sbmlsim
  • COMBINE standards are used whereever possible.

Visualization

  • interactive plots (altair)

Parallelization

  • simple parallelization of multiple simulation, collection of results

Parameter fitting

  • helpers for running parameter fitting experiments

Unit support

  • full support for units on model simulations