Simulation

Predict gene expression behavior with Kernel's genetic simulator.

What is Simulation?

The Simulator predicts:

• RNA polymerase flux

• Ribosome flux

• RNA concentrations

• Protein concentrations

These predictions help optimize construct design before experimental testing.

Running Simulations

From the Construct Editor

1. Open a construct

2. Click Sim. in the right sidebar

3. Configure simulation parameters

4. Click Run Simulation

Simulation Parameters

• Expression system: Host organism

• Copy number: Plasmid copy number

• Growth phase: Exponential, stationary

• Time course: Simulation duration

Understanding Results

RNA Polymerase Flux

Measures transcription activity:

• High flux = active transcription

• Bottlenecks indicate rate-limiting regions

• Compare across constructs

Ribosome Flux

Measures translation activity:

• Indicates protein production rate

• Identifies translation bottlenecks

• Affected by codon usage, mRNA structure

Concentration Predictions

Predicted steady-state levels:

• mRNA concentration

• Protein concentration

• Units and scale for comparison

Visualization

Results display as:

• Graphs over time

• Heatmaps along sequence

• Summary statistics

Interpreting Results

Good Design Indicators

• Smooth flux profiles

• High predicted expression

• No major bottlenecks

• Consistent with known biology

Potential Issues

• Flux drops indicate problems

• Low expression predictions

• Imbalanced multi-gene systems

• Unusual mRNA structures

Comparing Designs

Side-by-Side Comparison

1. Run simulations on multiple variants

2. Open runs in Runs section

3. Compare predictions

Design Iteration

1. Run initial simulation

2. Identify issues

3. Modify construct

4. Re-simulate

5. Compare improvements

Other Prediction Types

Signal Peptide Predictions

Predict secretion signal effectiveness:

• Signal peptide cleavage

• Secretion efficiency

• Recommended alternatives

Antibody Developability

For antibody constructs:

• Aggregation propensity

• Stability predictions

• Immunogenicity assessment

Run Management

Viewing Runs

1. Click Runs in the sidebar

2. See all simulation runs

3. Filter by type, date, status

Run Details

Each run shows:

• Input construct

• Parameters used

• Results and predictions

• Timestamp

Exporting Results

• Download predictions as CSV

• Export visualizations

• Share runs with collaborators

Best Practices

Before Simulation

• Verify construct is complete

• Check all annotations

• Confirm expression system matches design

Interpreting Results

• Consider predictions as estimates

• Compare relative differences

• Validate key designs experimentally

Iterative Design

• Use simulation to guide optimization

• Test multiple variants in silico

• Focus experiments on top candidates

Limitations

Simulations are predictive models:

• Based on known biology

• May not capture all effects

• Experimental validation recommended

• Continuously improving

Next Steps

• Compiler — Automated design

• Runs History — View all runs

• Codon Optimization — Optimize sequences