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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