BasiCO Documentation
BasiCO is a simplified interface to using COPASI from python. It is a collection of utility python scripts, that hide the complexity of the underlying SWIG generated language bindings.
The project is hosted on GitHub
Should you use basico in your project, please cite:
Bergmann, F. T. (2023). BASICO: A simplified Python interface to COPASI. Journal of Open Source Software, 8(90), 5553. https://doi.org/10.21105/joss.05553
Getting started
Examples
- Accessing Models from the database
- Creating and simulating a simple model
- Getting and setting reaction parameters and reactions
- Editing reaction kinetics
- Parameter Estimation
- Parameter estimation setup
- Parameter Estimation (import / export)
- Optimization
- Simple simulations and plotting
- Simulating a model with basico
- Simulating with custom results
- Parameter Scans
- Sensitivity Analysis
- Working with arrays of Compartments
- Using callbacks
- Working with Plots
- Working with Reports
- Working with SBML Ids
- Working with Annotations
- Working with
ipyparallel - Working with PEtab
- Model Selection
- Working with Parameter Sets
- Profile likelihood
- Metabolic Control Analysis
- Working with Widgets
- Retrieving all Task / Method Settings
- Linear Noise Approximation
API
Funding
This project has been possible thanks to LiBiS, the Baden-Württemberg Institute for Bioinformatics Infrastructure:
and to the BMBF funded de.NBI initiative (031L0104A, W-de.NBI-016):
