Team:Waterloo/Modeling/Intracellular Spread
Viral Spread Model
Plant Structure
-Plasmodesmata -Phloems/Vascular SystemVirus
-Initial Infection Sites -Founder Population -Viral Spread Rates -Viral Spread Chance -Viral AssemblyPlant Response
-SA Chance (Plant Defense) -Lysis Chance -SAR -SAR Spread ChanceBiological Background
Viral Spread Mechanisms
-Plasmodesmata -Phloem/Vascular SystemPlant Defense Mechanisms
-HR Apoptosis -SAR -Mechanisms -Signalling and SpreadSoftware Choice
Originally, three different agent-based modelling (ABM) software packages (MASON, MESA and Netlogo) were chosen out of several as the top candidates to create the viral spread simulation. All of the languages required for the simulation packages were unfamiliar to the team, and thus would have to be learned from scratch. Netlogo was chosen to create the final simulation due to a variety of its strengths as well as time constraints. Although Netlogo was the most unfamiliar-looking language, it presented itself as the simulation package with the smallest learning curve. Additionally, it had readily-available documentation and a built-in GUI. MESA was a Python-based simulation package and ultimately was not chosen due to its documentation not being as detailed or as readily available as MASON or Netlogo’s, as well as the level of familiarity with Python required to create the model being too high to achieve within the time constraints. MASON, a Java-based simulation package, despite having excellent, easily-found documentation did not have a built-in GUI, and did not have as many built in-functions as the Netlogo, thus requiring more work to get off the ground. Although in some cases the fewer amount of built-in functions could have proved to be an advantage (it would have added more flexibility and customization to the simulation), due to the time constraints and the demand of a level familiarity with Java (as with MESA) to create a simulation with MASON, Netlogo was thus chosen over MASON.