README

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