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SimEvolEnzCons (version 2.0.0)

data_sim: Simulation results for each constraint

Description

Six different datasets containing the simulation results for each constraint.

Usage

data("data_sim_SC")
data("data_sim_Comp")
data("data_sim_RegPos")
data("data_sim_RegNeg")
data("data_sim_CRPos")
data("data_sim_CRNeg")
data("data_sim_CRNeg_1grpNeg1sgl")
data("data_sim_RegNeg_1grpNeg1grpPos")

Arguments

Format

Each dataset is a list containing six elements:

$tabR

Dataframe of nsim*npt rows and (3*n+4) columns. Column $sim is the number of current simulation. Each row corresponds to the state at each observation step (i.e. after pasobs mutations), and columns are respectively concentrations (E1 to En), kinetic parameters (kin1 to kin_n), total concentration, total kinetic, flux, activities (A1 to An), and simulation number (column $sim)

$tabP_e

Numeric matrix of npt rows and n+1 columns, corresponding to relative concentrations at equilibrium (column 1 to n) at each observation step (in rows), and associated simulation number (column $sim)

$tabP_r

Same as $tabP_e, but for response coefficients

$list_init

List of 3 elements, containing initial values of concentrations in $E0, kinetic parameters in $kin0 and activities in $A0 for each simulation. Each element is a numeric matrix of nsim rows and n columns

$list_final

List of 3 elements, containing final values of concentrations in $E_f, kinetic parameters in $kin_f and activities in $A_f for each simulation. Each element is a numeric matrix of nsim rows and n columns

$param

List of input parameters:

  • n: number of enzymes,

  • nsim: number of simulation,

  • E0: matrix of initial concentrations, identical to $list_init$E0,

  • kin0: matrix of initial kinetic parameters, identical to $list_init$kin0,

  • Keq: numeric vector of constant equilibrium,

  • beta: matrix of co-regulation coefficients,

  • B: numeric vector of global co-regulation coefficients,

  • correl: character string indicating the constraint abbreviation,

  • N: population size,

  • pasobs: number of steps between two system observations,

  • npt: number of system observations,

  • X: parameter for flux computation,

  • Etot0: initial total concentration,

  • pmutA: probability for activity mutation,

  • other parameters are described in simul.evol.enz.multiple

Details

Possible constraints are listed below:

  • "SC": independence between all enzymes

  • "Comp": competition for resources

  • "RegPos": positive regulation

  • "RegNeg": negative regulation

  • "CRPos": competition plus positive regulation

  • "CRNeg": competition plus negative regulation

There is ten simulations by constraint.

Simulations differ by the initial concentrations (manually chosen), but initial concentrations are identical between constraints.

Chosen equilibrium for tabP_e and tabP_r are the theoretical equilibrium for constraints "SC", "Comp" and "RegPos", and the effective one for constraints "RegNeg", "CRPos" and "CRNeg".

These simulation results are exploited in Coton et al. (2021).

New datasets when there are regulation groups

"data_sim_CRNeg_1grpNeg1sgl" contains simulation results when there are one negative group and one singleton with competition.

"data_sim_RegNeg_1grpNeg1grpPos" contains simulation results when there are one negative and one positive groups, without competition.

References

Coton at al. (2021)