Generate mechanism-based hypotheses and design validation experiments. Use this skill to design control experiments (e.g., using nonsense mutations as knockouts) and reconstruct plasmid pathways (e.g., switching between pathway-level and enzyme-level analysis).
This skill assists in the scientific reasoning process by proposing specific experiments to test hypotheses about enzyme function and pathway dynamics.
Designs control experiments to validate findings or rule out artifacts. Specifically, it can identify and leverage nonsense mutations (STOP codons) within NNK libraries to serve as internal "knockout" controls for distinguishing true activity from background noise.
Usage:
import subprocess
import json
def design_control_experiment(experiment_type, library_context=None):
"""
Design a control experiment based on the hypothesis type.
Args:
experiment_type (str): Type of control needed (e.g., "nonsense_knockout", "wildtype_baseline").
library_context (dict): Context about the library (e.g., codon usage, positions).
Returns:
dict: Experimental design including selected variants and expected outcomes.
"""
cmd = [
"python",
"scripts/design_control_experiment.py",
"--type", experiment_type
]
if library_context:
cmd.extend(["--context", json.dumps(library_context)])
result = subprocess.run(cmd, capture_output=True, text=True)
return json.loads(result.stdout)
Designs molecular biology protocols to modify pathway architecture. It is used to transition between different experimental setups, such as removing a downstream enzyme (RhlB) to study the upstream enzyme (RhlA) in isolation.
Usage:
import subprocess
import json
def reconstruct_plasmid_pathway(operation, plasmid_map, target_gene):
"""
Design a protocol to reconstruct a plasmid pathway.
Args:
operation (str): Operation to perform (e.g., "remove_gene", "add_gene").
plasmid_map (str): Identifier or map of the source plasmid.
target_gene (str): Gene to target for the operation.
Returns:
dict: Protocol steps, primer designs, and verification methods.
"""
cmd = [
"python",
"scripts/reconstruct_plasmid_pathway.py",
"--op", operation,
"--plasmid", plasmid_map,
"--gene", target_gene
]
result = subprocess.run(cmd, capture_output=True, text=True)
return json.loads(result.stdout)
To find STOP codon variants in an NNK library at position 102:
python scripts/design_control_experiment.py --type "nonsense_knockout" --context '{"codon_scheme": "NNK", "target_residues": [102]}'
To design a Gibson assembly protocol to remove the RhlB gene from the pRhlAB plasmid:
python scripts/reconstruct_plasmid_pathway.py --op "remove_gene" --plasmid "pRhlAB" --gene "RhlB"