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Table 1 Agents, their movements and transformations

From: An agent-based model of the Notch signaling pathway elucidates three levels of complexity in the determination of developmental patterning

Agent ID Agent representation Movement and/or transformation Variable names within the code Variable descriptions
Nuc Cell nucleus static nuc_radius Radius size around nucleus
Mem Cell membrane static radius lipid-density Cell radius and position # of lipid agents
Dl Dl as initially transcribed Dl moves towards Mem and converts to Dlm delta-transcription-initial-rate Chance that a single Dl will be produced
Dlm Dl associated with membrane Dlm moves laterally from Mem to Mem Dlm converts Dlm’ delta-transform-time Time period before Dlm is converted to Dlm’
Dlm’ Dl form that interacts with N from another cell moves laterally from Mem to Mem Ages out deltaAge Time period a Dl will exist
N N as initially transcribed N moves towards Mem and converts to Nm notch-transcription-initial-rate Chance that a single N will be produced
Nm N associated with membrane, interacts with Dl from another cell, cleaved Nm moves laterally from Mem to Mem Nm converts to Nc when across from Dlm’ on another cell   
Nc Cleaved N moves from cell membrane to nucleus Nc converts to Nn when it reaches the nucleus notch-cleave-transport Sets randomness, direction and time frame of movement
Nn Nuclear form of N, transcription factor Ages out Alters N transcription Alters Dl transcription notchAge cleaved-nuc-notchcount Time period a N will exist Alters N and Dl initial transcription rates
  1. Agents are represented in bold print. Model commands are in italics