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Lineage Package
This documentation covers the cell-population simulation capabilities of Bioscrape as defined in the bioscrape.lineage package.
bioscrape.lineage is a wrapper around the original bioscrape.types and bioscrape.simulator packages that contains its own sets of objects and simulators (largely sub-classed from existing objects in bioscrape) designed to flexibly simulate growing, dividing (including stochastic partitioning of molecular species), and dying cell populations. Each individual cell is represented as a bioscrape CRN model with the ability to grow, divide, and die. Additionally, this package allows large ensembles of cells to be simulated efficiently offers flexible statistical wrappers (in development) to ensure that these simulations are of manageable size.
bioscrape.lineage supports SSA simulation and SSA with Delay Simulation of single cells. Cell lineages can be simulated via the following methods:
- Lineage Simulation: Beginning with an initial list of cells, the ensemble is simulated and all offspring and their time-course data is returned.
- Cell Propagation: Cells are propagated for a set amount of time. All cells states (living, dead optional) at the end of the simulation are returned. Time-course trajectories not stored.
- Single Cell Lineage: Beginning with a single cell, this cell is simulated with only one daughter cell being saved (chosen randomly) each division, resulting in a time-course set of data which tracks only a single cell at any time.
Cell growth, death, and division be modeled as Rule objects, which are evaluated every simulation step. There are 3 overarching Rule types: DivisionRules, VolumeRules, DeathRules. A number of different sub-classes exist
Alternatively, cell growth, death, and division can be modeled as Event Objects which fire according to an internal propensity. There are 3 overarching Event types: DivisionEvents, VolumeEvents, and DeathEvents.
As cells grow and divide, their internal species are re-partitioned according to VolumeSplitter objects which are associated with every DivisionRule and DivisionEvent.