Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
Analysis_MC4100_25C		Analysis_MC4100_25C
Analysis_MC4100_27C		Analysis_MC4100_27C
Analysis_MC4100_37C		Analysis_MC4100_37C
1-Taniuchi_data.ipynb		1-Taniuchi_data.ipynb
10-avg_filter.ipynb		10-avg_filter.ipynb
11.1-filter_app_no_log-PS1.ipynb		11.1-filter_app_no_log-PS1.ipynb
11.1B-filter_app-PS1.ipynb		11.1B-filter_app-PS1.ipynb
11.1B-filter_app_no_log-PS1.ipynb		11.1B-filter_app_no_log-PS1.ipynb
11.2-filter_app_no_log-PS2.ipynb		11.2-filter_app_no_log-PS2.ipynb
11.2B-filter_app-PS2.ipynb		11.2B-filter_app-PS2.ipynb
11.2B-filter_app_no_log-PS2.ipynb		11.2B-filter_app_no_log-PS2.ipynb
11.3-filter_app_no_log-PS3.ipynb		11.3-filter_app_no_log-PS3.ipynb
11.3B-filter_app-PS3.ipynb		11.3B-filter_app-PS3.ipynb
11.3B-filter_app_no_log-PS3.ipynb		11.3B-filter_app_no_log-PS3.ipynb
11.4-filter_app_no_log-PS4.ipynb		11.4-filter_app_no_log-PS4.ipynb
12-new_inf_method.ipynb		12-new_inf_method.ipynb
13-lsq-2-priors.ipynb		13-lsq-2-priors.ipynb
14-inf_on_lsq_fit.ipynb		14-inf_on_lsq_fit.ipynb
15-probabilistic-inf-using-LNA-ex-2.ipynb		15-probabilistic-inf-using-LNA-ex-2.ipynb
15-probabilistic-inf-using-LNA-ex-3.ipynb		15-probabilistic-inf-using-LNA-ex-3.ipynb
15-probabilistic-inf-using-LNA-ex-Tan.ipynb		15-probabilistic-inf-using-LNA-ex-Tan.ipynb
15-probabilistic-inf-using-LNA.ipynb		15-probabilistic-inf-using-LNA.ipynb
16-prob-inf-using-NUM-LNA-Tan-25.ipynb		16-prob-inf-using-NUM-LNA-Tan-25.ipynb
16-prob-inf-using-NUM-LNA-Tan-27.ipynb		16-prob-inf-using-NUM-LNA-Tan-27.ipynb
16-prob-inf-using-NUM-LNA-Tan-37.ipynb		16-prob-inf-using-NUM-LNA-Tan-37.ipynb
16b-prob-inf-using-NUM-LNA-TRvol_dep.ipynb		16b-prob-inf-using-NUM-LNA-TRvol_dep.ipynb
16c-prob-inf-using-NUM-LNA-BSvol_dep.ipynb		16c-prob-inf-using-NUM-LNA-BSvol_dep.ipynb
16d-prob-inf-using-NUM-LNA-Mixed-voldep-again.ipynb		16d-prob-inf-using-NUM-LNA-Mixed-voldep-again.ipynb
16d-prob-inf-using-NUM-LNA-Mixed-voldep.ipynb		16d-prob-inf-using-NUM-LNA-Mixed-voldep.ipynb
2a-FPM_and_EGR-37.ipynb		2a-FPM_and_EGR-37.ipynb
2b-FPM_and_EGR-27.ipynb		2b-FPM_and_EGR-27.ipynb
2c-FPM_and_EGR-25.ipynb		2c-FPM_and_EGR-25.ipynb
3-SSA_sim_fn.ipynb		3-SSA_sim_fn.ipynb
4-Simulator_fn_play_around.ipynb		4-Simulator_fn_play_around.ipynb
5-first_inf_on_concentrations.ipynb		5-first_inf_on_concentrations.ipynb
6-inference_from_SSA.ipynb		6-inference_from_SSA.ipynb
7-inf_on_gens.ipynb		7-inf_on_gens.ipynb
8-prob_dist_obj_fn.ipynb		8-prob_dist_obj_fn.ipynb
9-new_distance_fn-more_particles-no_log.ipynb		9-new_distance_fn-more_particles-no_log.ipynb
9-new_distance_fn-more_particles.ipynb		9-new_distance_fn-more_particles.ipynb
9-new_distance_fn.ipynb		9-new_distance_fn.ipynb
DataProcessing-25.nb		DataProcessing-25.nb
DataProcessing-27.nb		DataProcessing-27.nb
DataProcessing-37.nb		DataProcessing-37.nb
GFsol.nb		GFsol.nb
MN_props.csv		MN_props.csv
MN_props_25.csv		MN_props_25.csv
MN_props_27.csv		MN_props_27.csv
README.md		README.md
SSA_file.jl		SSA_file.jl
exp_grs_all.csv		exp_grs_all.csv
exp_grs_all_25.csv		exp_grs_all_25.csv
exp_grs_all_27.csv		exp_grs_all_27.csv
extract_gens.jl		extract_gens.jl

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Tanouchi-inference

We show using maximum likelihood inference (in Julia) that bacterial proteins are kept at an approximate homeostasis.

Go through the ipynb's in numerical order to understand the project. We find that it is the combined transcriptional/translation rate of the proteins and not the burst size that scales linearly with the volume. This volume dependence keeps the E. coli approximately at homeostasis. All experimental data used comes from: Tanouchi, Yu, et al. "Long-term growth data of Escherichia coli at a single-cell level." Scientific data 4.1 (2017): 1-5.

jamesholehouse/Tanouchi-inference

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Tanouchi-inference

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