COPASI

Create a new COPASI model and define the enzymatic reaction.

Set the initial concentrations of substrate and enzyme.

Define the kinetic rate law (e.g., Michaelis-Menten kinetics).

Run a time course simulation and plot the concentrations of substrate and product.

Analyze the results to determine the reaction rate and equilibrium.

Load an SBML model of the metabolic pathway.

Import experimental data (e.g., time series of metabolite concentrations).

Define the parameters to be estimated.

Configure the parameter estimation task with appropriate optimization algorithm and settings.

Run the parameter estimation and analyze the results to obtain the best-fit parameter values.

Validate the model with the estimated parameters against independent experimental data.

Create a COPASI model of the gene expression network.

Define the reactions involved in transcription and translation.

Set the appropriate kinetic rate laws.

Run a stochastic simulation using Gillespie's algorithm.

Analyze the simulation results to observe fluctuations in mRNA and protein levels.

Calculate statistical measures of noise (e.g., coefficient of variation).

Load an SBML model of the circadian clock network.

Define the model parameters (e.g., degradation rates, transcription rates).

Run a time course simulation and observe the oscillations of clock genes and proteins.

Analyze the period and amplitude of the oscillations.

Investigate the effects of perturbations on the circadian rhythm (e.g., light exposure).

Load an SBML model of the signaling pathway.

Define the drug target and its mechanism of action (e.g., inhibition of a specific enzyme).

Simulate the pathway with and without the drug.

Compare the simulation results to assess the effects of the drug on pathway activity.

Identify potential biomarkers for drug response.