Python implementation of simulations for Caltech class BE/CS/CNS/Bi 191a.
Note: To run examples in examples/, run python -m examples/<file> or cp to root directory of projcet.
Dependencies:
- Python 3.5.1
- Python-Scipy 0.16.1-2
- Python-Numpy 1.10.4-1
List of current features:
- Continuous CRN
- Stochastic CRN
- matplotlib.pyplot Plotting to both file and screen
- Print Trajectory
- Constructor takes either list/list(string) for reagants/reactions instead of dict/list(tuple).
- Syntax parser for reactions
- Simulation setups can be toString() and fromFile()
- Simulation results are not written to file to save space.
- Reversible Reactions
- Subsample for plotting
- Python plotting very slow for large lists.
List of planned features (in rough order of priority, not necessarily difficulty):
- Enumerator for DSDs
- Better error messages when failure, more edge cases
- Interactive Front End
- Automatically create reagants and set to 0 in add_reactions?
- Need incremental mutators rather than just setBLAH
- Loading/Saving simulation object to file
- Adaptive Stepsize
Changelog:
- 02/29/16 -- Reversibile reactions, subsampled plotting
- 02/27/16 -- Removed some unnecessary dict lookups
- Load from file, print string (can save to file)
- 02/11/16 -- Set up syntax parser for both reactions and reagants.
- Set up stochastic Simulation child class
- 02/09/16 -- Set up continuous Simulation child class
- 02/07/16 -- Set up base Simulation abstract class