Table 1 Description of kboolnet toolkit scripts, their inputs, and their outputs
Type | Name | Description | Inputs | Outputs |
|---|---|---|---|---|
Simulation engine | BoolNetSim.R | Used by all the VVV modules below. Simulates a model using the BoolNet package [21] given an initial state and set of nodes to inhibit/activate | Model file, initial state, on-list, off-list | Resulting simulation trajectory and attractor as a CSV and a PDF |
Verification | VerifyModel.R | Simulates a model under a set of activators and inhibitors while repeatedly toggling a given ligand on and off to check consistency of the resulting attractors | Model file, set of runs with list including initial state, on-list, off-list, and toggled ligand for each run | RData file holding trajectories and attractors for all rounds of simulation, CSVs and PDFs of consolidated trajectories, and XGMML graphs of the state spaces |
Validation | TruthTable.R | Simulates a model under all possible combinations of given inhibitors and activators and sees their effect on a set of output nodes | Model file, nodes to activate or inhibit, output nodes, initial state | Truth table PDF/CSV |
ScoreNet.R | Simulates a model under the perturbations encoded in a database of experimental data and sees how closely the simulation reflects real-world observations | MIDAS-format experimental database, model file | Mean square error for model, PDFs for experimental results, simulation results, and comparison of the two | |
SensitivityAnalysis.R | Measures effect of individually inhibiting every node on the effect a ligand has on a set of output nodes | Model file, ligand to toggle, initial state, outputs to monitor | PDF showing semi-quantitative effect of inhibition on ligand to output signal | |
Visualization | AnimatePath.R | Animates the regulatory graph of a model using a given trajectory CSV | Regulatory graph, trajectory CSV | Animation GIF |
PlotModules.R | Makes individual regulatory graphs of each of modules stored in a model file | Model file, list of modules to plot | Regulatory graph XGMML for each module | |
PlotPath.R | Plots a trajectory CSV | Trajectory CSV | Plot as PDF | |
PlotPathComparison.R | Aligns two trajectories/attractors and plots an overlay of the two showing (dis)similarities between the two | Two trajectory/attractor CSVs | Comparison plot as PDF |