Run a Simulation

Configure and execute simulations with custom parameters.

Time estimate: 15 minutes

Goal

By the end of this tutorial, you’ll be able to:

• Configure simulation time settings
• Modify initial conditions and parameters
• Monitor simulation progress
• Handle common simulation issues

Starting a Run

From any model detail page or lab page:

1. Open the lab you want to run
2. Open the run configuration panel
3. Configure settings (see below)
4. Click Start Run

Configuration Options

Time Settings

Initial Conditions

Override the default starting values for supported model inputs:

# Example
prey: 100 → 150
predator: 10 → 20

Use the form fields exposed by the lab or model package.

Parameter Overrides

Modify model parameters without editing the model:

# Example
alpha: 1.0 → 1.5
beta: 0.1 → 0.08

Remote Size

For labs that require a GPU-backed remote size, Biosimulant automatically disables CPU-only sizes and blocks incompatible remote submissions before the run starts.

Monitoring Progress

After starting a run:

1. Status indicator shows current state:

   • 🟡 Queued
   • 🔵 Running
   • 🟢 Completed
   • 🔴 Failed

2. Progress and logs may be shown while the run is active, depending on your account or workspace

Run States

Handling Failures

Common Error: Numerical Instability

Symptoms: “Integration failed” or “NaN values”

Solutions:

• Reduce simulation duration
• Decrease output points
• Check for extreme parameter values
• Use a different integration method (if available)

Common Error: Timeout

Symptoms: “Simulation timed out”

Solutions:

• Reduce duration or complexity
• Break into smaller runs
• Contact support for long-running simulations

Common Error: Invalid Parameters

Symptoms: “Parameter out of bounds”

Solutions:

• Check parameter constraints in model documentation
• Reset to default values
• Use biologically reasonable values

Repeating a Run

The most reliable way to compare scenarios is:

1. Start from the same lab
2. Change one parameter or configuration block
3. Start a new run
4. Compare the finished runs in the results view

Best Practices

1. Start simple: Run with defaults first, then modify
2. Document changes: Note which parameters you changed
3. Save configurations: Bookmark configurations you use frequently
4. Compare systematically: Change one parameter at a time

Programmatic Runs

For automation, use the desktop CLI for desktop-managed labs or the Biosimulant library for local Python workflows.

Next Steps

• Analyze Results - Visualize your simulation
• Biosimulant Library - Automate simulations with Python