Simulation

Model simulation in Catalax is centered around generating synthetic datasets from biochemical models. This guide covers the essential workflow: creating models, running simulations, and analyzing results through the Dataset interface.

Core Workflow

The simulation process follows a straightforward pattern:

1. Define a Model: Create species and differential equations
2. Create a Dataset: Set up initial conditions
3. Configure Simulation: Define time parameters
4. Run Simulation: Generate time-series data
5. Analyze Results: Plot and evaluate the data

Step 1: Creating a Biochemical Model

Start by defining your biochemical system:

import catalax as ctx

# Create a model
model = ctx.Model(name="Enzyme Kinetics")

# Add species
model.add_species("S")  # Substrate

# Define the differential equation
model.add_ode("S", "-v_max * S / (K_m + S)")

# Set parameter values
model.parameters["v_max"].value = 7.0
model.parameters["K_m"].value = 100.0

The model automatically infers parameters (v_max, K_m) from the equation and creates Parameter objects that you can configure.

Step 2: Setting Up Initial Conditions

Create a Dataset linked to your model and add initial conditions:

# Create an empty dataset from the model
dataset = ctx.Dataset.from_model(model)

# Add single initial condition
dataset.add_initial(S=300.0)

# Add multiple initial conditions for comparison
for concentration in [50.0, 100.0, 200.0, 400.0]:
    dataset.add_initial(S=concentration)

print(f"Dataset has {len(dataset.measurements)} initial conditions")

Each call to add_initial() creates a new Measurement in the dataset with the specified initial conditions.

Step 3: Configuring the Simulation

Define simulation parameters using SimulationConfig:

# Basic simulation configuration
config = ctx.SimulationConfig(
    t0=0,        # Start time
    t1=100,      # End time  
    nsteps=50    # Number of time points
)

Key parameters:

• t0, t1: Start and end times for simulation
• nsteps: Number of time points in the output
• dt0: Initial step size (default: 0.1)
• rtol, atol: Numerical tolerances (defaults: 1e-5)

Step 4: Running the Simulation

Once you have defined your model, set up initial conditions, and configured the simulation parameters, you can execute the simulation to generate time-series data. The simulation process integrates the differential equations forward in time, starting from each set of initial conditions:

# Run simulation
simulated_dataset = model.simulate(dataset, config)

# The result is a new Dataset with time-series data
print(f"Generated {len(simulated_dataset.measurements)} trajectories")

# Each measurement now contains time-series data
measurement = simulated_dataset.measurements[0]
print(f"Time points: {len(measurement.time)}")
print(f"Species data: {list(measurement.data.keys())}")

The simulate() method is the core function that transforms your initial conditions into complete time-series trajectories. It returns a new Dataset object where each Measurement has been populated with simulation results. Each measurement now contains three key components:

• time: An array of time points from t0 to t1 with the specified number of steps
• data: A dictionary mapping each species name to its concentration time-series
• initial_conditions: The original initial values that were used to start this trajectory

This structure means that your simulation results are immediately ready for analysis, plotting, and integration with other Catalax workflows.

Step 5: Visualization and Analysis

Basic Plotting

Catalax datasets come with built-in plotting capabilities that make it easy to visualize your simulation results. The plotting system automatically handles multiple trajectories and provides clean, publication-ready figures:

# Plot all trajectories
simulated_dataset.plot(show=True)

# Plot specific measurements
simulated_dataset.plot(
    measurement_ids=[simulated_dataset.measurements[0].id, 
                     simulated_dataset.measurements[1].id],
    show=True
)

The plot() method creates a multi-panel figure where each panel shows one simulation trajectory. When you plot all trajectories at once, you can easily compare how different initial conditions lead to different system behaviors, which is particularly useful for understanding concentration-dependent effects in biochemical systems.

Model Evaluation

One of the most powerful features of the Catalax plotting system is the ability to compare model predictions with experimental data by passing a predictor to the plot function. This enables direct visual assessment of how well your model captures the observed behavior:

# Create some "experimental" data (or load real data)
experimental_data = model.simulate(dataset, config)

# Evaluate how well a fitted model predicts the data
experimental_data.plot(predictor=model, show=True)

When you pass a predictor to the plot function, Catalax automatically generates model predictions at the same time points as your experimental data and overlays them on the same plot. This creates a comprehensive visualization that shows both the experimental observations and the model’s predictions, making it immediately clear how well the model captures the system behavior. The plot displays experimental data as points or lines while model predictions appear as smooth overlaid curves, providing an intuitive visual comparison to assess model fit quality.

Quantitative Evaluation

Beyond visual assessment, Catalax provides quantitative metrics to evaluate model performance numerically. The metrics() method calculates comprehensive fit statistics that help you assess model quality objectively:

# Get comprehensive fit statistics
metrics = experimental_data.metrics(model)
print(f"RMSE: {metrics.rmse:.3f}")
print(f"R²: {metrics.r2:.3f}")
print(f"AIC: {metrics.aic:.1f}")

These metrics provide different perspectives on model performance: RMSE (Root Mean Square Error) quantifies the average prediction error, R² indicates the proportion of variance explained by the model, and AIC (Akaike Information Criterion) balances model fit against complexity. Together, these statistics give you a comprehensive understanding of how well your model captures the experimental data.

Practical Examples

Example 1: Parameter Study

Understanding how parameter changes affect system behavior is a fundamental aspect of biochemical modeling. This example demonstrates how to systematically compare different parameter values to understand their impact on system dynamics:

# Create base model
model = ctx.Model(name="Parameter Study")
model.add_species("S")
model.add_ode("S", "-v_max * S / (K_m + S)")

# Test different v_max values
v_max_values = [5.0, 7.0, 10.0]
results = []

for v_max in v_max_values:
    model.parameters["v_max"].value = v_max
    model.parameters["K_m"].value = 100.0
    
    # Same initial conditions
    dataset = ctx.Dataset.from_model(model)
    dataset.add_initial(S=200.0)
    
    # Simulate
    result = model.simulate(dataset, config)
    results.append(result)

# Plot comparison
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
for i, result in enumerate(results):
    meas = result.measurements[0]
    ax.plot(meas.time, meas.data["S"], label=f"v_max = {v_max_values[i]}")
ax.legend()
ax.set_xlabel("Time")
ax.set_ylabel("Substrate Concentration")
plt.show()

Example 2: Generating Synthetic Data

Synthetic data generation is essential for developing and testing new analysis methods, validating computational approaches, and training machine learning models. This example shows how to create realistic synthetic datasets that mimic experimental conditions and include appropriate variability:

import numpy as np

# Set up model with realistic parameters
model = ctx.Model(name="Synthetic Data Generator")
model.add_species("S")
model.add_ode("S", "-v_max * S / (K_m + S)")
model.parameters["v_max"].value = 7.0
model.parameters["K_m"].value = 100.0

# Create dataset with varied initial conditions
dataset = ctx.Dataset.from_model(model)

# Add systematic variation in initial conditions
for base_conc in [50.0, 100.0, 200.0, 300.0]:
    for replicate in range(5):
        # Add small random variation
        noisy_conc = np.random.normal(base_conc, base_conc * 0.02)
        dataset.add_initial(S=noisy_conc)

# Simulate synthetic data
synthetic_data = model.simulate(dataset, config)

# Export for sharing
synthetic_data.to_croissant("./data", name="enzyme_kinetics_synthetic")

Example 3: Model Validation

Model validation is crucial for ensuring that your computational model accurately represents the biological system you’re studying. This example demonstrates how to test model accuracy by comparing predictions against known data, which is essential for building confidence in your modeling results:

# Generate "true" data with known parameters
true_model = ctx.Model(name="True System")
true_model.add_species("S")
true_model.add_ode("S", "-v_max * S / (K_m + S)")
true_model.parameters["v_max"].value = 7.0
true_model.parameters["K_m"].value = 100.0

# Create test dataset
test_dataset = ctx.Dataset.from_model(true_model)
test_dataset.add_initial(S=200.0)

# Generate "experimental" data
experimental_data = true_model.simulate(test_dataset, config)

# Create model with different parameters (to test fitting)
fitted_model = true_model.model_copy()
fitted_model.parameters["v_max"].value = 6.5  # Slightly wrong
fitted_model.parameters["K_m"].value = 110.0  # Slightly wrong

# Compare models visually
experimental_data.plot(predictor=fitted_model, show=True)

# Get quantitative comparison
metrics = experimental_data.metrics(fitted_model)
print(f"Model fit quality: RMSE = {metrics.rmse:.3f}")

Working with Real Data

For comprehensive information about importing data from various formats, managing datasets, and data augmentation techniques, see the Data Management guide. This covers importing from EnzymeML documents, pandas DataFrames, Croissant archives, and various data processing workflows.

Model as Predictor

An important feature of the Catalax design is that any Model can serve as a Predictor, which creates a unified interface for model evaluation and comparison. This means that whether you’re working with mechanistic models, neural ODEs, or hybrid approaches, they all implement the same prediction interface. This allows models to be used seamlessly for plotting model curves over experimental data, calculating fit metrics for model validation, and serving as components in parameter estimation workflows.

Best Practices

Following these best practices will help you develop robust and reliable simulation workflows:

1. Start simple: Begin with single species and basic kinetics before adding complexity. This approach helps you understand the fundamental behavior of your system and makes it easier to diagnose issues when they arise.

2. Check parameters: Always verify that parameter values are reasonable for your biological system. Parameters should fall within ranges that make sense given the physical and chemical constraints of your system.

3. Use multiple initial conditions: Test model behavior across the full range of relevant concentration conditions. This helps you understand how your system responds under different scenarios and can reveal important features like saturation effects or threshold behaviors.

4. Visualize results: Always plot your simulations to check for reasonable behavior. Visual inspection can quickly reveal issues like unphysical oscillations, incorrect steady states, or parameter values that lead to unrealistic dynamics.

5. Save your work: Export datasets in Croissant format for sharing and reproducibility. This standardized format ensures that your data can be easily shared with collaborators and used in different analysis pipelines.

This simulation framework provides the foundation for all advanced Catalax workflows, including parameter optimization, Bayesian inference, and neural network training. By mastering these basic simulation concepts, you’ll be well-prepared to tackle more sophisticated modeling challenges.