Knockout

The knockout module provides utilities for simulating in silico knockouts of biological processes and generating all possible knockout combinations. It is designed to work with parameter vectors representing biological systems.

Features

• Apply Knockouts:
  Modify parameter vectors to simulate knockouts for transcription, translation, or phosphorylation processes.

• Generate Knockout Combinations:
  Create all possible combinations of knockouts, including individual phosphorylation site knockouts.

Functions

apply_knockout

Simulates knockouts by modifying a given parameter vector.

• Parameters:
• base_params (np.ndarray): Original parameter vector.
• knockout_targets (dict): Specifies processes to knock out (transcription, translation, phosphorylation).

• num_psites (int): Number of phosphorylation sites.

• Returns:
  A modified parameter vector with the specified knockouts applied.

generate_knockout_combinations

Generates all possible combinations of knockouts for transcription, translation, and phosphorylation.

• Parameters:

• num_psites (int): Number of phosphorylation sites.

• Returns:
  A list of dictionaries, each representing a unique knockout combination.