runscripts/paper/paper_runs.sh
# Script to run simulations used to generate data for figures in the paper
# Data will be uncompressed to allow running of new analysis scripts
# Requires setup outlined in requirements.txt and in README.md
# Suggestion: run one set at a time by commenting out all other fw_queue.py lines

lpad reset
make clean compile

## Parameter sensitivity analysis
runscripts/paper/sensitivity.sh sensitivity 0 20000

## Set A - basal condition
# Used for figure 4
DESC="SET A 32 gens 8 seeds basal with growth noise and D period" \
VARIANT="wildtype" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=0 \
SINGLE_DAUGHTERS=1 N_GENS=32 N_INIT_SIMS=8 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
python runscripts/fireworks/fw_queue.py

## Set B - nutrient shift from minimal to minimal + AA
# Used for figure 1
DESC="SET B 9 gens 8 seeds shift to plus AA without growth noise with D period" \
VARIANT="nutrientTimeSeries" FIRST_VARIANT_INDEX=2 LAST_VARIANT_INDEX=2 \
SINGLE_DAUGHTERS=1 N_GENS=9 N_INIT_SIMS=8 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=0 D_PERIOD_DIVISION=1 \
python runscripts/fireworks/fw_queue.py

## Set C - 3 growth rates from different conditions
# Used for figure 2
DESC="SET C 4 gens 256 seeds 3 conditions with growth noise and D period" \
VARIANT="condition" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=2 \
SINGLE_DAUGHTERS=1 N_GENS=4 N_INIT_SIMS=256 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
RUN_AGGREGATE_ANALYSIS=0 \
python runscripts/fireworks/fw_queue.py

## Set D - changes to RNAP and ribosome expression
# Used for figure 2
# Misc. options consistent with Set C

# This subset of simulations is redundant with the first variant of Set C
DESC="SET D1 4 gens 256 seeds" \
VARIANT="wildtype" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=0 \
SINGLE_DAUGHTERS=1 N_GENS=4 N_INIT_SIMS=256 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
DISABLE_RIBOSOME_CAPACITY_FITTING=0 DISABLE_RNAPOLY_CAPACITY_FITTING=0 \
RUN_AGGREGATE_ANALYSIS=0 \
python runscripts/fireworks/fw_queue.py

DESC="SET D2 4 gens 256 seeds, unfit ribosome expression" \
VARIANT="wildtype" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=0 \
SINGLE_DAUGHTERS=1 N_GENS=4 N_INIT_SIMS=256 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
DISABLE_RIBOSOME_CAPACITY_FITTING=1 DISABLE_RNAPOLY_CAPACITY_FITTING=0 \
RUN_AGGREGATE_ANALYSIS=0 \
python runscripts/fireworks/fw_queue.py

DESC="SET D3 4 gens 256 seeds, unfit rna poly expression" \
VARIANT="wildtype" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=0 \
SINGLE_DAUGHTERS=1 N_GENS=4 N_INIT_SIMS=256 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
DISABLE_RIBOSOME_CAPACITY_FITTING=0 DISABLE_RNAPOLY_CAPACITY_FITTING=1 \
RUN_AGGREGATE_ANALYSIS=0 \
python runscripts/fireworks/fw_queue.py

DESC="SET D4 4 gens 256 seeds, unfit ribosome and rna poly expression" \
VARIANT="wildtype" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=0 \
SINGLE_DAUGHTERS=1 N_GENS=4 N_INIT_SIMS=256 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
DISABLE_RIBOSOME_CAPACITY_FITTING=1 DISABLE_RNAPOLY_CAPACITY_FITTING=1 \
RUN_AGGREGATE_ANALYSIS=0 \
python runscripts/fireworks/fw_queue.py

## Set E - metabolism objective weighting
# Used for figure 3
DESC="SET E 8 gens 8 seeds 10 metabolism weighting values" \
VARIANT="metabolism_kinetic_objective_weight" FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=9 \
SINGLE_DAUGHTERS=1 N_GENS=8 N_INIT_SIMS=8 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=0 D_PERIOD_DIVISION=0 \
python runscripts/fireworks/fw_queue.py

## Set F - MenE expression
# Used in supplemental figure
DESC="SET_F 8 gens 8 seeds 9 menE expression values" \
VARIANT=meneParams FIRST_VARIANT_INDEX=0 LAST_VARIANT_INDEX=8 \
SINGLE_DAUGHTERS=1 N_GENS=8 N_INIT_SIMS=8 \
MASS_DISTRIBUTION=1 GROWTH_RATE_NOISE=1 D_PERIOD_DIVISION=1 \
python runscripts/fireworks/fw_queue.py


## Launch the fireworks created with fw_queue.py
# Uncomment one method - rlaunch is interactive, qlaunch is distributed
# rlaunch rapidfire
# qlaunch -r rapidfire --nlaunches infinite --sleep 5 --maxjobs_queue 100
