Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
data		data
figures		figures
old		old
.gitignore		.gitignore
0_catalyst_test.ipynb		0_catalyst_test.ipynb
0_potential_topics.ipynb		0_potential_topics.ipynb
1_phase_plane_trajectory.ipynb		1_phase_plane_trajectory.ipynb
1_re-parameterization.ipynb		1_re-parameterization.ipynb
2_auto_classifier_1.ipynb		2_auto_classifier_1.ipynb
2_auto_classifier_2_FP_detection.ipynb		2_auto_classifier_2_FP_detection.ipynb
2_auto_classifier_3_thresholds.ipynb		2_auto_classifier_3_thresholds.ipynb
2_auto_classifier_4_full_algo_and_SD_map.ipynb		2_auto_classifier_4_full_algo_and_SD_map.ipynb
2_auto_classifier_5_explore_SD_map.ipynb		2_auto_classifier_5_explore_SD_map.ipynb
2_jump_process_bug.ipynb		2_jump_process_bug.ipynb
3_modifying_core_model.ipynb		3_modifying_core_model.ipynb
3_time_sharing_simu.ipynb		3_time_sharing_simu.ipynb
4_SD_map_remake.ipynb		4_SD_map_remake.ipynb
4_a_look_into_non_cooperative.ipynb		4_a_look_into_non_cooperative.ipynb
4_dynamic_vignettes.ipynb		4_dynamic_vignettes.ipynb
4_forced_bistability.ipynb		4_forced_bistability.ipynb
4_het_activation_time.ipynb		4_het_activation_time.ipynb
5_anti_correlation_examples.ipynb		5_anti_correlation_examples.ipynb
5_ultrasensitivity_schematic.ipynb		5_ultrasensitivity_schematic.ipynb
6_remake_of_fixpoint_detection.ipynb		6_remake_of_fixpoint_detection.ipynb
README.md		README.md
SD_new_n1_50.jld2		SD_new_n1_50.jld2
SD_new_n1_50_to2000.jld2		SD_new_n1_50_to2000.jld2
SD_ssa_n1_b50_rt5.jld2		SD_ssa_n1_b50_rt5.jld2
SD_ssa_n1_b50_rt5_1000to2000.jld2		SD_ssa_n1_b50_rt5_1000to2000.jld2
SD_ssa_n1_b50_rt5_to1000.jld2		SD_ssa_n1_b50_rt5_to1000.jld2
SD_ssa_n3_b100_rt5.pdf		SD_ssa_n3_b100_rt5.pdf
SD_ssa_n3_b100_rt5_to2000.jld2		SD_ssa_n3_b100_rt5_to2000.jld2
SD_ssa_n3_b50_rt02.jld2		SD_ssa_n3_b50_rt02.jld2
SD_ssa_n3_b50_rt02.pdf		SD_ssa_n3_b50_rt02.pdf
SD_ssa_n3_b50_rt10_m2.jld2		SD_ssa_n3_b50_rt10_m2.jld2
SD_ssa_n3_b50_rt10_m2.pdf		SD_ssa_n3_b50_rt10_m2.pdf
SD_ssa_n3_b50_rt2_5_m2.jld2		SD_ssa_n3_b50_rt2_5_m2.jld2
SD_ssa_n3_b50_rt2_5_m2.pdf		SD_ssa_n3_b50_rt2_5_m2.pdf
SD_ssa_n3_b50_rt5.jld2		SD_ssa_n3_b50_rt5.jld2
SD_ssa_n3_b50_rt5_5000toend.jld2		SD_ssa_n3_b50_rt5_5000toend.jld2
SD_ssa_n3_b50_rt5_lts.jld2		SD_ssa_n3_b50_rt5_lts.jld2
SD_ssa_n3_b50_rt5_lts_5000toend.jld2		SD_ssa_n3_b50_rt5_lts_5000toend.jld2
SD_ssa_n3_b50_rt5_lts_to5000.jld2		SD_ssa_n3_b50_rt5_lts_to5000.jld2
SD_ssa_n3_b50_rt5_m2.jld2		SD_ssa_n3_b50_rt5_m2.jld2
SD_ssa_n3_b50_rt5_m2_to2000.jld2		SD_ssa_n3_b50_rt5_m2_to2000.jld2
SD_ssa_n3_b50_rt5_to5000.jld2		SD_ssa_n3_b50_rt5_to5000.jld2
accumulated_het_act_both_non_bs.jld2		accumulated_het_act_both_non_bs.jld2
bifurcation_data_Esigma1_kons1.jld2		bifurcation_data_Esigma1_kons1.jld2
bifurcation_forced.pdf		bifurcation_forced.pdf
bifurcation_forced_bk.pdf		bifurcation_forced_bk.pdf
dominance_curve.pdf		dominance_curve.pdf
fraction_act_both_non_bs.pdf		fraction_act_both_non_bs.pdf
het_activation_both_non_us.pdf		het_activation_both_non_us.pdf
hist_e_occu_both_nonus_kd80_Rt50_koff01.pdf		hist_e_occu_both_nonus_kd80_Rt50_koff01.pdf
k1_KS_map_20.jld2		k1_KS_map_20.jld2
k1_KS_map_20.pdf		k1_KS_map_20.pdf
simu_dual_utils.jl		simu_dual_utils.jl
simu_utils.jl		simu_utils.jl
traj_both_nonus_kd80_Rt50_koff01.pdf		traj_both_nonus_kd80_Rt50_koff01.pdf
traj_forced_bs_k1_00022_Rt50.pdf		traj_forced_bs_k1_00022_Rt50.pdf
traj_forced_bs_k1_0004_Rt50.pdf		traj_forced_bs_k1_0004_Rt50.pdf
traj_no_comp_both_k1_00001_Rt200.pdf		traj_no_comp_both_k1_00001_Rt200.pdf
traj_sto_switching_n1.pdf		traj_sto_switching_n1.pdf

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Modelling bacterial alternative sigma factors and their competition

This is the code for my Master's thesis, which shows that various dynamical behaviours of the alternative sigma factor are permitted by a simple stochastic model based on molecular details.

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Modelling bacterial alternative sigma factors and their competition

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Modelling bacterial alternative sigma factors and their competition

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