GINsim

Define nodes representing key proteins and genes involved in the cell cycle.

Establish regulatory interactions (activations, inhibitions) between these components.

Encode logical rules defining the responses of each node to its regulators.

Simulate the model using asynchronous updating policies.

Analyze the state transition graph to identify stable states corresponding to different cell cycle phases.

Import an existing model of the regulatory network.

Define a perturbation representing the loss-of-function of the target gene.

Simulate the perturbed model.

Compare the state transition graph of the perturbed model with that of the original model.

Identify changes in stable states and attractors to assess the impact of the knockout.

Model the disease-related regulatory network.

Identify regulatory circuits and their functional sub-spaces.

Simulate the effects of perturbations targeting different components.

Analyze the changes in stable states and attractors to identify potential drug targets.

Validate the identified targets through in-vitro experiments.

Represent signaling molecules and their interactions as nodes and arcs in the model.

Define logical rules that describe the activation and inhibition of downstream targets.

Simulate the model with different input signals.

Analyze the resulting state transition graph to understand how the signal propagates through the pathway.

Identify potential feedback loops and their impact on signal amplification and duration.

Model the regulatory network controlling cellular differentiation.

Define stable states corresponding to different cell types.

Simulate the model with different initial conditions.

Analyze the state transition graph to identify the pathways that lead to different cell fates.

Investigate the role of key transcription factors in driving differentiation.