This package provides infrastructure for analyzing SBML models using Tellurium. The scope includes:
- convenient access to static model inforation (parameters, species, reactions)
- support for retrieving and setting values of parameters
- creating a roadrunner from any source that roadrunner supports using a single constructor
- common data structure for simulation results
- flexible and simplified plotting
The main class is Model, an analysis abstraction for an SBML model.
Key properties are:
roadrunner: a roadrunner object- species_names: a list of all species names
- reaction_names: a list of all reaction names
- parameter_names: a list of all parameter names
Key methods are:
- simulate(start_time, end_time, points_per_time, variables)->Timeseries
- set(name, value) - set a name to a value
- get(name) - retrieve the value of a name
- getTime(): returns the current simulation time
- setTime(time): runs the simulation from time 0 to the specified time
- diagram: display a diagram of the reaction network
The Timeseries class provides a way to contain data taken from the same times
- Timeseries(dataframe)
- mat2TS: converts a matrix to a timeseries
- A bug in Tellurium makes it fail on 3.10. So, need to back level
python to 3.9.
sudo apt install python3.x-venv. More details at link
- Version 0.1.1 (current)
- Model: get, set, simulate, serialize, copy
- Parameter: constructor
- Timeseries: construct
- plotOneTS, plotManTS
- Fixed Timeseries so that it handles computed values
- Model.simulate can add noise to the result
- Iterate on BioModels