Overview

Mission: make SBML simulations simple

The idea of sbmlsim is to provide a simple abstraction layer for running simulations with SBML models in python and simplify common tasks occuring in modeling.

Simplicity

  • make it easy to encode 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 whenever possible.

Visualization

  • plots and reports

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