Description Usage Arguments Value Author(s)
Creates a infrastructure required to simulate kappa model with various parameter sets and generate correspondent folder infrastructure
1 2 3 4 5 6 | prepareProject(project = NA, numSets = 500, pTable, constantfiles = c("main_rnap_def_rule.ka",
"main_rnap_init.ka", "main_rnap_param.ka"), templatefiles = c("var_prom_def.ka",
"var_prom_init.ka", "var_prom_rule.ka"), paramfile = c("var_prom_param.ka"),
k_min = 0.1, k_max = 10, exec.path = "~/kasim3/KaSim", shFile = NA,
jobFile = NA, jobCFile = NA, repReg = "_-", type = c("parallel",
"concurrent", "both"), writeDir = FALSE)
|
project |
name of the project to be created, new folder will be created to contain the project files, if not specified multi_current_date stub will be used. |
numSets |
number of parameter sets to be generated |
pTable |
Parameter ranges data frame. Should contain columns |
constantfiles |
list of file names containing constant part of the model |
templatefiles |
list of template file names to be used to create model |
paramfile |
list of parameter file names |
k_min |
minimum parameter value factor to be used if |
k_max |
maximum parameter value factor to be used if |
exec.path |
path to kappa language simulator executables in simulation environment |
shFile |
run script template file name |
jobFile |
job management job file template |
jobCFile |
job management job template file for concurrent simulations |
repReg |
regular expression to be replaced with number of parameter set |
type |
type of the project |
writeDir |
if TRUE project directory and its content will be created |
project object
Anatoly Sorokin
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