The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
The Decaying-Dimerization Reaction Set (Gillespie 2001) consists of three species and four reaction channels.
S1 --c1--> 0
S1 + S1 --c2--> S2
S2 --c3--> S1 + S1
S2 --c4--> S3Define parameters
library(GillespieSSA2)
sim_name <- "Decaying-Dimerizing Reaction Set"
final_time <- 10
params <- c(c1 = 1.0, c2 = 0.002, c3 = 0.5, c4 = 0.04)
initial_state <- c(s1 = 10000, s2 = 0, s3 = 0)Define reactions
reactions <- list(
reaction("c1 * s1", c(s1 = -1)),
reaction("c2 * s1 * s1", c(s1 = -2, s2 = +1)),
reaction("c3 * s2", c(s1 = +2, s2 = -1)),
reaction("c4 * s2", c(s2 = -1, s3 = +1))
)Run simulations with the Exact method
set.seed(1)
out <- ssa(
initial_state = initial_state,
reactions = reactions,
params = params,
final_time = final_time,
method = ssa_exact(),
sim_name = sim_name
)
plot_ssa(out)
Run simulations with the Explict tau-leap method
set.seed(1)
out <- ssa(
initial_state = initial_state,
reactions = reactions,
params = params,
final_time = final_time,
method = ssa_etl(tau = 0.003),
sim_name = sim_name
)
plot_ssa(out)
Run simulations with the Binomial tau-leap method
set.seed(1)
out <- ssa(
initial_state = initial_state,
reactions = reactions,
params = params,
final_time = final_time,
method = ssa_btl(),
sim_name = sim_name
)
plot_ssa(out)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.