Example notebooks#
Minimal table of contents and notes for running the notebooks in this folder.
Forward simulations:#
- Simulation Examples: simulation-examples.ipynb
- CME <> ODE <> SDE Conversion: model-conversion.ipynb
Optimization and inference:#
- Simple Gene Expression Model: simple-gene-expression.ipynb
- Positive Self-Loop Gene Expression: gene-positive-self-loop.ipynb
- Simple Entropy Maximization: MaxEnt-positive-self-loop.ipynb
Other examples:#
- Protein folding dwell/path cost: protein-fold-dwell-path-cost.ipynb
- Queuing M/M/1 simulation: queuing-mm1-simulation.ipynb