Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

Software for multi-valued logic and formal concept analysis

The R scripts in the zip file below perform simulations of a (biological) model in multi-valued logic. The output time series can be transformed to a transition context, a data structure of formal concept analysis (FCA). This context is readable by standard FCA software like Concept Explorer, in order to visualize (a part of) the simulations and to generate dynamical rules by attribute exploration.

The main script "ROSInflammationSim.r" implements specific interaction rules in multi-valued logic, with different time scales, starting from a table of initial states "startBile.csv". Different experimental conditions and model variants can be chosen by Boolean variables at the head of the script, similarly a plot of the time courses for all or selected variables. The standard output is a csv table listing the sequence of the simulated states.

To construct the FCA data structure, this script calls "transitionContext.r", which can also be used independently to compute a transition context from data in the format of BoothDataDiscrete.csv.

The R scripts were developed for Wollbold J, Jaster R, M