Multi-Scale Model of CRISPR-Induced Coevolutionary Dynamics v0.3 CC0 1.0 Universal (CC0 1.0) Code Authors: Joshua Weitz and Lauren Childs (2011-2012) Contact: Joshua Weitz Assistant Professor School of Biology Georgia Institute of Technology Atlanta GA 30332 Email: jsweitz@gatech.edu The objective of this code is to develop a flexible framework for considering the co-evolutionary dynamics of hosts and viruses which interact via a CRISPR immune mechanism. The code is written in Matlab. The simulation should be run by modifying script_master.m and by changing default parameters in the datasets/ directory NOTE: To get started, type in >> ExampleRunwithPlotting.m at the Matlab prompt which will run a short-time simulation and plot the results (population densities and strain counts). The simulation should take less than 5 minutes to run on a reasonably modern desktop/laptop. The complete outfile file for this example will be generated in: ./Output/Spacer8Proto10_LongTime1.mat Additional files included are: calc_valid_spacers.m create_bacteria.m create_virus.m crispr_events.m estimate_mutrate_LMC.m event_bacteria_deletion.m event_bacteria_mutate_LMC.m event_species_death.m event_virus_mutate_LMC.m infection_matrix.m infection_rules.m master_evolve_LMC.m mut_crispr_LMC.m parsave.m parsave_inprogram.m protospacer_select.m script_master.m set_initial_conditions.m Trial datasets in the directory 'datasets/'