Returns the default CARNIVAL options as a list. You can modify the elements of the list and then use it as an argument in run_COSMOS_metabolism_to_signaling or run_COSMOS_signaling_to_metabolism. If you choose CPLEX or CBC, you must modify then the solverPath field and point to the CPLEX/CBC executable (See Details).

## Usage

default_CARNIVAL_options(solver = NULL)

## Arguments

solver

one of cplex (recommended, but require 3rd party tool), cbc (also require 3rd party tool) or lpSolve (only for small networks)

## Value

returns a list with all possible options implemented in CARNIVAL. see the documentation on runCARNIVAL.

## Details

COSMOS is dependent on CARNIVAL for exhibiting the signalling pathway optimisation. CARNIVAL requires the interactive version of IBM Cplex, Gurobi or CBC-COIN solver as the network optimiser. The IBM ILOG Cplex is freely available through Academic Initiative here. Gurobi license is also free for academics, request a license following instructions here. The CBC solver is open source and freely available for any user, but has a significantly lower performance than CPLEX or Gurobi. Obtain CBC executable directly usable for cosmos here. Alternatively for small networks, users can rely on the freely available lpSolve R-package, which is automatically installed with the package.

## Examples

# load and change default options:
my_options = default_CARNIVAL_options(solver = "cplex")

my_options$solverPath = "/Applications/CPLEX_Studio128/cplex/bin/x86-64_osx/cplex" my_options$threads = 2
my_options\$timelimit = 3600*15