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

• Getting Started
  • Installation
  • Use the package
  • Loading a Model
  • Interrogating the Model
  • Analyzing the Model
  • Saving a Model

Examples

• Accessing Models from the database
  • BioModels
  • JWS Online
• Creating and simulating a simple model
• Getting and setting reaction parameters and reactions
  • Load model
  • Getting/setting global quantities
  • Getting/setting species (metabolites)
  • Getting/setting reaction parameters
  • Getting/setting reactions
  • Setting scheme
  • Setting reaction name
• Editing reaction kinetics
• Parameter Estimation
• Parameter estimation setup
  • preparing the data
  • setting up the parameter estimation
  • Constraints
• Parameter Estimation (import / export)
  • The Format
  • Example
• Optimization
  • Model
  • The Setup
  • Running the optimization
  • Customn Output
  • Constraints
• Simple simulations and plotting
  • Load a model
  • Run time course
  • Get compartments
  • Get parameters (“global quantities”)
  • Run steady state
  • Use pandas syntax for indexing and plotting
• Simulating a model with basico
  • The run_time_course command
• Simulating with custom results
  • Simulations:
  • Custom Selection list
  • Custom Time Points
  • For expert users
• Parameter Scans
  • Modifying Scan Settings
  • Runnin a scan:
• Sensitivity Analysis
  • Settings
  • Running the Analysis
• Working with arrays of Compartments
  • Linear arrays of compartments
  • Creating 2D array of compartments
• Using callbacks
  • Timeouts
• Working with Plots
• Working with Reports
  • Retrieving Report Definitions
  • Adding Reports
  • Changing values
  • Assigning to task
• Working with SBML Ids
• Working with Annotations
  • Resource Lists / Updating
  • Displaying Annotations:
  • Setting annotations
• Working with ipyparallel
• Working with PEtab
• Model Selection
• Working with Parameter Sets
  • Looking at parameter sets
  • Creating / Modifying Parameter sets
  • Removing parameter sets
  • Parameter sets and Parameter Estimation
• Profile likelihood
  • Preparing files
  • Processing the files:
  • Looking at the results
  • Everything together
• Metabolic Control Analysis
• Working with Widgets
• Retrieving all Task / Method Settings
• Linear Noise Approximation

API

• basico
  • basico package