This is a single cell agent-based model of BK virus (BKV) replicating within a salivary gland cell. You'll see replication and transcription of viral proteins using host cell machinery. The 3-D assembly of encapsidated BKV and non-infectious particles is also modeled. Capsid formation is modeled using boids. How cool is that?
CytoNuc.java: Builds ABM with agents below. Rules are scheduled on odd ticks. Maintenance (add or remove agents) is scheduled on even ticks. This is because rules cannot be removed from the scheduler within a currently executing rule.
DNAPol.java: Host
Genome.java: Virus
HostGenome.java: Host
LgTAg.java: Virus
MRNA.java: Host
Ribosome.java: Host
SmTAg.java: Virus
TranscriptionFactor.java: Host
VLP.java: Virus
VP1.java: Virus
VP123.java: Virus
VP2.java: Virus
VP3.java: Virus
AgentGeometry.java: A lot of methods are not used (yet) but implementation for geometric scaling,
rotations and transformations
AgentMove.java: Move algorithms
AgentProbabilities.java: All rule probabilities are in here
AgentStyle3D.java: Define colors of agents for display
BoundToConverter.java: to convert enum class to string for proper display
GStateConverter.java: ditto
LocationConverter.java: ditto
MStateConverter.java: ditto
MTypeConverter.java: ditto
MyContinuous3DProjectionDecorator.java: to facilitate drawing circles in projection
MyContinuousProjectionDescriptor.java: ditto
MyProjectionDecoratorFactory.java: ditto