reTASEP - TASEP with reinitiation Implementation of the totally asymmetric simple exclusion process (TASEP) with reinitiation and particles of arbitrary size. requirements: C++-compiler (g++) that supports C++11 usage: 1. compile with "make" 2. set parameters in file "parameters.inp" 3. start "./reTASEP" Detailed usage: "./reTASEP parameterfile value=key value2=xyz ..." The parameterfile has one Key=Value pair per line, comments start with a '#'. mandatory keys: alpha, beta, gamma, k, lambda, t_max, dt, no_runs, mode, detailed_output. run modes "mode=...": standard run: 0; exp. dist. lifetime: 1; exp. dist.+fixed lifetime: 2; single slow codon: 4-6; read RNA file, but av. elongation rate: 8. output modes "detailed_output=...": 0 -> standard output: density, av. number of proteins 1 -> detailed output: also print density and yield for each run 2 -> time evolution density 3 -> time evolution yield 4 -> time evolution <density> <yield/time> <total yield until that time> 5 -> print av. occupation per codon optional keys (pick one of them!): length, RNA_filename. example: ./simRNAtransl parameters.inp alpha=0.1 beta=0.5