This file provides guidance to run the simulations used in Salvi et al 2020.

If you wish to use this code to perform your own, new simulations, either:
1: Change the paramter settings in the header files found in the include directory, or
2: Change the source code in the program files itself.

If you simply wish to rerun (a subset of) the simulations used in this work, please use the provided start-run.py.

By default, the start_run.py script will take a Param_config.hh file provided from include/Param_config_options/ and place the output in runs

Below is an overview of the simulations used per figure in the paper. Some simulations are used multiple times.
The script will note when you have already started a simulation with the header you intend to use and not start that simulation
If you do want that simulation to run, please provide your own output directory name.

Figures not named do not have simulations associated with them.

To run the simulation for Figure 4B, go to the Salvi_model directory, and call the python script from the commandline as:

python start_run.py ARR1_knockout_Param_config.hh

This will start the simulation at Salvi_model/runs/ARR1_knockout


/////////////////////////////////////////////
Main text figures:

> Figure 4B,E:
ARR1_knockout_Param_config.hh

> Figure 5H,I:
ARR1_knockout_Param_config.hh
ARR12_knockout_Param_config.hh

> Figure 6A:
ARR1_knockout_Param_config.hh
ARRs_No_auxin_induction_config.hh
> Figure 6C:
ARR12_auxin_effect_isolated_Param_config.hh
ARR12_PLT_effect_isolated_Param_config.hh
ARR1ARR12_double_knockout_Param_config.hh
ARR1_knockout_Param_config.hh

> Figure 7:
WT_Param_config.hh
KRP2_ARR1_EFFECT_KNOCKOUT_Param_config.hh
ARR12_knockout_Param_config.hh
ARR1_knockout_Param_config.hh
ARR1ARR12_double_knockout_Param_config.hh

/////////////////////////////////////////////

Supplemental figures

> Figure S3A,D:
No_Divisions_No_growth.hh
> Figure S3B,C:
No_Dilution_config.hh
> Figure S3E:
lowPLT_start_config.hh
lowPLT_start_Compensate_extra_PLT_production_config.hh
> Figure S3F:
WT_Param_config.hh

> Figure S5A,B:
ARR1ARR12_double_knockout_Param_config.hh
> Figure S5C:
WT_Param_config.hh
ARRs_No_auxin_induction_PLTS_compensating_config.hh

/////////////////////////////////////////////

If you want to run novel parameters,
write or modify your own Param_config.hh and/or other header files,
or change the .cc files, make sure to run both:

Make clean
Make

before starting your newly written program to make sure it compiles correctly.