This function takes a series of SBtab tables, as returned by
SBtabVFGEN::sbtab_from_tsv() and creates GillespieSSA2 reactions
from them. Reactions arfe made pairwise, as forward and backward
reaction pairs. If a backward reaction doesn't exist, the list item
is NULL. A valid set of reactions can be obtained with !is.null(reactions)
Usage
makeGillespieModel(SBtab, LV = NULL, strip.null = TRUE)
Arguments
- SBtab
a series of tables as returned by sbtab_from_tsv()
- LV
is the product of Avogadro's constant L and the system's
volume V in litres; if unspecified this information is retrieved
from the SBtab files, if missing we assume 1µm³ of volume (the
approximate sizes of bacteria or synapses)
Value
a list of reactions
Examples
# model.tsv <- dir(pattern="[.]tsv$")
# model.sbtab <- SBtabVFGEN::sbtab_from_tsv(model.tsv)
# reactions <- makeGillespieModel(model.sbtab)
# l <- is.null(reactions)
# model.ssa2 <- reactions[!l]