Building

1. Clone the repository
2. Create conda environment from given .yml mamba env create -f environment.yml
3. Activate simulator environment mamba activate simulator
4. Build the application sh compile.sh
5. Run the application
   ./Build/bin/simulator data/examples/glycolysis_selfmade.json

Build with Clion

See (isssue14)[#14]

Running

The application can be configured via the config.json.

threads: Determines the amount of instances of the program that will run. Will create the appropriate output files for each instance.

mode: iteration or stopping_criterion. If iteration is choosren the simulation we run for the given number of iterations. If stopping_criterion is choosen the simulation will stop once the given threshold is reached OR the std. deviation is below the threshold given in stdDevThresh.

iterations: Determines for how many iterations the simulation will run in both modes. Note that in stopping_criterion mode the simulation might end earlier.

history_length: Determines the length of the history that will be taken into account for the std. deviation.

stdDevThresh: Determines at which low the std. dev is allowed to be for the last history_length iterations. Note: If at least one metaboltie shows a bigger std. deviation the simulation will continue to run.

Analyzing

1. Execute the plot script python3 scripts/plot.py
2. Execute the analysis script Rscript analysis.R