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Basic Usage

The Jupyter Notebook Tutorials are a great place to get started with Cellnition.

The general workflow to create NFSMs in Cellnition comprises 6 main steps:

  1. Define via edges (user-defined or imported), or procedurally generate a regulatory network as a directed graph in a computationally-agnostic, Continuous, or Boolean oriented computational workflow.
  2. Characterize the graph to automatically categorize input, output & internal nodes, along with other features such as cycles and node hierarchical level.
  3. Build a computational model of the regulatory network for Continuous or Boolean models.
  4. Use the computational model in a state machine to identify all unique equilibrium output states for each input state via state space search available for Continuous or Boolean models.
  5. Create the NFSMs in Continuous or Boolean systems. Cellnition does this by starting the system in each equilibrium state, applying each input state, and determining the equilibrium state that the system transitions to.
  6. Output, plot, and analyze the resulting Network Finite State Machines!