Skip to main content

Table 4 Summary of output files/directories created for each ChemChains experiment.

From: ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists

File/Directory Name Description
allNodes_avg.mtb Tab-delimited text file with activation levels of all nodes across all simulations
input_dosages.csv Activity levels of all external inputs across all simulations
patternNodes_avg.csv Activity levels of nodes specified for pattern analysis. (Created only during pattern analysis)
input_labels.csv List of external input nodes
node_labels.csv Names of all nodes in the network
specs.txt Simulation specification file used for this experiment
logic/ Directory containing all logic files associated with this experiment
nodesAvg/ Directory containing activity level information for each node
snapshotAnalysis/ Directory to hold node activity information obtained from multiple points in the course of a simulation
patterns/ Output directory for the patterns extension
bits/ Output directory holding ON/OFF sequences for all nodes in the network