Run the following make commands from kale/make.

• make pt_data1: Run MCMC fitting (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bid_bim_nbd_release/mcmc

• make pt_data1_norm: Run MCMC fitting with a Gaussian prior distribution for the NBD fluorescence scaling parameters (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bid_bim_nbd_release/mcmc_norm_prior

• make nbd_labeling_ratios_table

• make pt_data2_fret: Run MCMC fitting with coupled NBD and FRET dynamics (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bid_bim_fret_nbd_release/fret_mcmc. (54 fits)

• make pt_data2_fret_norm: Run MCMC fitting with coupled NBD and FRET dynamics with a Gaussian prior distribution for the NBD fluorescence scaling parameters (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bid_bim_fret_nbd_release/fret_mcmc_norm. (54 fits)

• make pt_data3_fret: Run MCMC fitting with coupled NBD and FRET dynamics (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bax_bax_fret_nbd_release/fret_mcmc. (27 fits)

• make pt_data3_fret_norm: Run MCMC fitting with coupled NBD and FRET dynamics with a Gaussian prior distribution for the NBD fluorescence scaling parameters (requires Starcluster setup). Files are stored in tbidbaxlipo/plots/bax_bax_fret_nbd_release/fret_mcmc_norm. (27 fits)

• Building "stoplight" plot (do for both fret_mcmc and fret_mcmc_norm):

  • python process_3conf_mcmc_submit.py fret_mcmc/*. Run from bax_bax_fret_nbd_release directory to generate density files after fitting.
  • (From fret_mcmc directory): python ../plot_k1_k2_dists.py assemble ...
    • ... k1 *.k1_hist
    • ... k2 *.k2_hist
    • ... c1 *.c1_scaling
    • ... c2 *.c2_scaling
    • ... f1 *.fret1_scaling
    • ... f2 *.fret2_scaling
  • (From fret_mcmc directory): python ../plot_k1_k2_dists.py plot ...
    • ... k1k2 fret_Bid_k1_density_mx.txt fret_Bid_k2_density_mx.txt pt_data3_k1k2
    • ... c1c2 fret_Bid_c1_density_mx.txt fret_Bid_c2_density_mx.txt pt_data3_c1c2
    • ... f1f2 fret_Bid_f1_density_mx.txt fret_Bid_f2_density_mx.txt pt_data3_f1f2

python ../plot_k1_k2_dists.py assemble k1 *.k1_hist
python ../plot_k1_k2_dists.py assemble k2 *.k2_hist
python ../plot_k1_k2_dists.py assemble c1 *.c1_scaling
python ../plot_k1_k2_dists.py assemble c2 *.c2_scaling
python ../plot_k1_k2_dists.py assemble f1 *.fret1_scaling
python ../plot_k1_k2_dists.py assemble f2 *.fret2_scaling

# For fret_mcmc:
python ../plot_k1_k2_dists.py plot k1k2 fret_Bid_k1_density_mx.txt fret_Bid_k2_density_mx.txt pt_data3_k1k2
python ../plot_k1_k2_dists.py plot c1c2 fret_Bid_c1_density_mx.txt fret_Bid_c2_density_mx.txt pt_data3_c1c2
python ../plot_k1_k2_dists.py plot f1f2 fret_Bid_f1_density_mx.txt fret_Bid_f2_density_mx.txt pt_data3_f1f2

# For fret_mcmc_norm:
python ../plot_k1_k2_dists.py plot k1k2 fret_norm_Bid_k1_density_mx.txt fret_norm_Bid_k2_density_mx.txt pt_data3_norm_k1k2
python ../plot_k1_k2_dists.py plot c1c2 fret_norm_Bid_c1_density_mx.txt fret_norm_Bid_c2_density_mx.txt pt_data3_norm_c1c2
python ../plot_k1_k2_dists.py plot f1f2 fret_norm_Bid_f1_density_mx.txt fret_norm_Bid_f2_density_mx.txt pt_data3_norm_f1f2

• make all: Equivalent to building all of the following targets:

  • make bax_bax_fret: Bax-Bax FRET Pilot Dataset (141203)

  • make nbd_release: Generates the following plots:

    • Raw and normalized NBD fluorescence endpoint bar plots
    • Raw and WT-normalized permeabilization endpoint bar plots
    • Others...

  • make fret_nbd_release: Generates the following plots:

    • Raw and normalized NBD fluorescence endpoint bar plots
    • Raw and WT-normalized permeabilization endpoint bar plots
    • Others...