├── ECHO_handling_scripts ├── .ipynb_checkpoints │ ├── completed_concentration-checkpoint.ipynb │ ├── concentration_to_volume-checkpoint.ipynb │ ├── extract_yield-checkpoint.ipynb │ ├── named_volumes_to_concentrations-checkpoint.ipynb │ └── volume_to_echo-checkpoint.ipynb ├── README.md ├── completed_concentration.ipynb ├── concentration_to_volume.ipynb ├── example │ ├── concentrations_example.csv │ ├── concentrations_example_completed.csv │ ├── concentrations_line_A.csv │ ├── concentrations_line_A_completed.csv │ ├── concentrations_line_P.csv │ ├── concentrations_line_P_completed.csv │ ├── example_TECAN.csv │ ├── example_aa.csv │ ├── example_comments.txt │ ├── example_concentrations_reconstituted.csv │ ├── example_draw_mean.csv │ ├── example_draw_ratio.csv │ ├── example_draw_std.csv │ ├── example_everything.csv │ ├── example_instructions.csv │ ├── example_named_volumes.csv │ ├── example_outliers.csv │ ├── example_volumes.csv │ ├── example_water.csv │ ├── example_yield_and_std.csv │ ├── line_A_concentrations_reconstituted.csv │ ├── line_A_named_volumes.csv │ ├── line_A_volumes.csv │ ├── line_P_concentrations_reconstituted.csv │ ├── line_P_named_volumes.csv │ └── line_P_volumes.csv ├── example_original │ ├── concentrations_example.csv │ ├── concentrations_example_completed.csv │ ├── concentrations_line_A.csv │ ├── concentrations_line_A_completed.csv │ ├── concentrations_line_P.csv │ ├── concentrations_line_P_completed.csv │ ├── example_TECAN.csv │ ├── example_aa.csv │ ├── example_comments.txt │ ├── example_concentrations_reconstituted.csv │ ├── example_draw_mean.csv │ ├── example_draw_ratio.csv │ ├── example_draw_std.csv │ ├── example_everything.csv │ ├── example_instructions.csv │ ├── example_named_volumes.csv │ ├── example_outliers.csv │ ├── example_volumes.csv │ ├── example_water.csv │ ├── example_yield_and_std.csv │ ├── line_A_concentrations_reconstituted.csv │ ├── line_A_named_volumes.csv │ ├── line_A_volumes.csv │ ├── line_P_concentrations_reconstituted.csv │ ├── line_P_named_volumes.csv │ └── line_P_volumes.csv ├── extract_yield.ipynb ├── named_volumes_to_concentrations.ipynb └── volume_to_echo.ipynb ├── README.md ├── active_learning_loop ├── .ipynb_checkpoints │ ├── generate_model_statistics-checkpoint.ipynb │ ├── initial_plate_generation-checkpoint.ipynb │ └── learn_and_suggest-checkpoint.ipynb ├── README.md ├── data │ ├── no_controls │ │ ├── plate_AL_10_raw_yield_and_std.csv │ │ ├── plate_AL_1_raw_yield_and_std.csv │ │ ├── plate_AL_2_raw_yield_and_std.csv │ │ ├── plate_AL_3_raw_yield_and_std.csv │ │ ├── plate_AL_4_raw_yield_and_std.csv │ │ ├── plate_AL_5_raw_yield_and_std.csv │ │ ├── plate_AL_6_raw_yield_and_std.csv │ │ ├── plate_AL_7_raw_yield_and_std.csv │ │ ├── plate_AL_8_raw_yield_and_std.csv │ │ └── plate_AL_9_raw_yield_and_std.csv │ ├── plate_AL_10_raw_everything.csv │ ├── plate_AL_1_raw_everything.csv │ ├── plate_AL_2_raw_everything.csv │ ├── plate_AL_3_raw_everything.csv │ ├── plate_AL_4_raw_everything.csv │ ├── plate_AL_5_raw_everything.csv │ ├── plate_AL_6_raw_everything.csv │ ├── plate_AL_7_raw_everything.csv │ ├── plate_AL_8_raw_everything.csv │ └── plate_AL_9_raw_everything.csv ├── echo_files │ └── initial_plate.csv ├── generate_model_statistics.ipynb ├── initial_plate_generation.ipynb ├── learn_and_suggest.ipynb ├── model_statistics │ ├── iteration_10fold_1.png │ ├── iteration_10fold_2.png │ ├── iteration_10fold_3.png │ ├── iteration_10fold_4.png │ ├── iteration_10fold_5.png │ ├── iteration_1fold_1.png │ ├── iteration_1fold_2.png │ ├── iteration_1fold_3.png │ ├── iteration_1fold_4.png │ ├── iteration_1fold_5.png │ ├── iteration_2fold_1.png │ ├── iteration_2fold_2.png │ ├── iteration_2fold_3.png │ ├── iteration_2fold_4.png │ ├── iteration_2fold_5.png │ ├── iteration_3fold_1.png │ ├── iteration_3fold_2.png │ ├── iteration_3fold_3.png │ ├── iteration_3fold_4.png │ ├── iteration_3fold_5.png │ ├── iteration_4fold_1.png │ ├── iteration_4fold_2.png │ ├── iteration_4fold_3.png │ ├── iteration_4fold_4.png │ ├── iteration_4fold_5.png │ ├── iteration_5fold_1.png │ ├── iteration_5fold_2.png │ ├── iteration_5fold_3.png │ ├── iteration_5fold_4.png │ ├── iteration_5fold_5.png │ ├── iteration_6fold_1.png │ ├── iteration_6fold_2.png │ ├── iteration_6fold_3.png │ ├── iteration_6fold_4.png │ ├── iteration_6fold_5.png │ ├── iteration_7fold_1.png │ ├── iteration_7fold_2.png │ ├── iteration_7fold_3.png │ ├── iteration_7fold_4.png │ ├── iteration_7fold_5.png │ ├── iteration_8fold_1.png │ ├── iteration_8fold_2.png │ ├── iteration_8fold_3.png │ ├── iteration_8fold_4.png │ ├── iteration_8fold_5.png │ ├── iteration_9fold_1.png │ ├── iteration_9fold_2.png │ ├── iteration_9fold_3.png │ ├── iteration_9fold_4.png │ ├── iteration_9fold_5.png │ ├── iteration_results.csv │ └── iteration_results_small.csv └── models_statistics_small │ ├── iteration_10fold_1.png │ ├── iteration_10fold_2.png │ ├── iteration_10fold_3.png │ ├── iteration_10fold_4.png │ ├── iteration_10fold_5.png │ ├── iteration_1fold_1.png │ ├── iteration_1fold_2.png │ ├── iteration_1fold_3.png │ ├── iteration_1fold_4.png │ ├── iteration_1fold_5.png │ ├── iteration_2fold_1.png │ ├── iteration_2fold_2.png │ ├── iteration_2fold_3.png │ ├── iteration_2fold_4.png │ ├── iteration_2fold_5.png │ ├── iteration_3fold_1.png │ ├── iteration_3fold_2.png │ ├── iteration_3fold_3.png │ ├── iteration_3fold_4.png │ ├── iteration_3fold_5.png │ ├── iteration_4fold_1.png │ ├── iteration_4fold_2.png │ ├── iteration_4fold_3.png │ ├── iteration_4fold_4.png │ ├── iteration_4fold_5.png │ ├── iteration_5fold_1.png │ ├── iteration_5fold_2.png │ ├── iteration_5fold_3.png │ ├── iteration_5fold_4.png │ ├── iteration_5fold_5.png │ ├── iteration_6fold_1.png │ ├── iteration_6fold_2.png │ ├── iteration_6fold_3.png │ ├── iteration_6fold_4.png │ ├── iteration_6fold_5.png │ ├── iteration_7fold_1.png │ ├── iteration_7fold_2.png │ ├── iteration_7fold_3.png │ ├── iteration_7fold_4.png │ ├── iteration_7fold_5.png │ ├── iteration_8fold_1.png │ ├── iteration_8fold_2.png │ ├── iteration_8fold_3.png │ ├── iteration_8fold_4.png │ ├── iteration_8fold_5.png │ ├── iteration_9fold_1.png │ ├── iteration_9fold_2.png │ ├── iteration_9fold_3.png │ ├── iteration_9fold_4.png │ ├── iteration_9fold_5.png │ └── iteration_results_small.csv ├── compounds_effect_analysis ├── .ipynb_checkpoints │ ├── compound_effect_analysis-checkpoint.ipynb │ ├── linear_analysis-checkpoint.ipynb │ ├── mutual_information-checkpoint.ipynb │ ├── mutual_information_analysis-checkpoint.ipynb │ └── quantitative_analysis-checkpoint.ipynb ├── AB │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── AB_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── DH5_alpha │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── DH5_alpha_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── ORI │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── ORI_full │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── ORI_full_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── ORI_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── PS │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── PS_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── README.md ├── data │ ├── AB │ │ └── 102_points.csv │ ├── DH5_alpha │ │ └── 102_points.csv │ ├── ORI │ │ └── 102_points.csv │ ├── ORI_full │ │ ├── no_controls │ │ │ ├── plate_AL_10_raw_yield_and_std.csv │ │ │ ├── plate_AL_1_raw_yield_and_std.csv │ │ │ ├── plate_AL_2_raw_yield_and_std.csv │ │ │ ├── plate_AL_3_raw_yield_and_std.csv │ │ │ ├── plate_AL_4_raw_yield_and_std.csv │ │ │ ├── plate_AL_5_raw_yield_and_std.csv │ │ │ ├── plate_AL_6_raw_yield_and_std.csv │ │ │ ├── plate_AL_7_raw_yield_and_std.csv │ │ │ ├── plate_AL_8_raw_yield_and_std.csv │ │ │ └── plate_AL_9_raw_yield_and_std.csv │ │ ├── plate_AL_10_raw_everything.csv │ │ ├── plate_AL_1_raw_everything.csv │ │ ├── plate_AL_2_raw_everything.csv │ │ ├── plate_AL_3_raw_everything.csv │ │ ├── plate_AL_4_raw_everything.csv │ │ ├── plate_AL_5_raw_everything.csv │ │ ├── plate_AL_6_raw_everything.csv │ │ ├── plate_AL_7_raw_everything.csv │ │ ├── plate_AL_8_raw_everything.csv │ │ └── plate_AL_9_raw_everything.csv │ ├── PS │ │ └── 102_points.csv │ ├── rifaximin │ │ └── 102_points.csv │ └── spectinomycin │ │ └── 102_points.csv ├── linear_analysis.ipynb ├── mutual_information_analysis.ipynb ├── rifaximin │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png ├── rifaximin_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── spectinomycin │ ├── coefficents_from_lin_reg.png │ ├── coefficents_from_lin_reg_intercept.png │ ├── coefficents_from_linear.csv │ ├── lin_reg_fold_1.png │ ├── lin_reg_fold_2.png │ ├── lin_reg_fold_3.png │ ├── lin_reg_fold_4.png │ └── lin_reg_fold_5.png └── spectinomycin_mi │ ├── coefficents_from_mi.csv │ └── mutual_information.png ├── controls_analysis_plates ├── data_AB │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ ├── regression_AB_AB_to_ORI_yieldreg_ref.png │ │ └── regression_AB_to_ORI_AB_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_AB_with_ORI.csv │ ├── duplicates │ │ ├── duplicated_AB_AB_to_ORI_yield.png │ │ └── duplicated_AB_to_ORI_AB_yield.png │ ├── extracting_duplicates.ipynb │ ├── normalised_AB_data.csv │ └── raw_data │ │ ├── AB_comments.txt │ │ ├── AB_concentrations_reconstituted.csv │ │ ├── AB_draw_mean.csv │ │ ├── AB_draw_ratio.csv │ │ ├── AB_draw_std.csv │ │ ├── AB_everything.csv │ │ ├── AB_outliers.csv │ │ ├── AB_yield_and_std.csv │ │ └── tecan_results.csv ├── data_DH5_alpha │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ ├── regression_DH5_DH5_to_ORI_yieldreg_ref.png │ │ └── regression_DH5_to_ORI_DH5_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_DH5_with_ORI.csv │ ├── duplicates │ │ ├── duplicated_DH5_DH5_to_ORI_yield.png │ │ └── duplicated_DH5_to_ORI_DH5_yield.png │ ├── extracting_duplicates.ipynb │ ├── normalised_DH5.csv │ └── raw_data │ │ ├── DH5_comments.txt │ │ ├── DH5_concentrations_reconstituted.csv │ │ ├── DH5_draw_mean.csv │ │ ├── DH5_draw_ratio.csv │ │ ├── DH5_draw_std.csv │ │ ├── DH5_everything.csv │ │ ├── DH5_outliers.csv │ │ ├── DH5_yield_and_std.csv │ │ └── tecan_results.csv ├── data_PS │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ ├── regression_PS_full_PS_to_ORI_yieldreg_ref.png │ │ └── regression_PS_to_PS_PS_to_ORI_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_PS.csv │ ├── duplicates │ │ ├── duplicated_PS_full_PS_to_ORI_yield.png │ │ ├── duplicated_PS_full_PS_to_PS_yield.png │ │ └── duplicated_PS_to_PS_PS_to_ORI_yield.png │ ├── extracting_duplicates.ipynb │ ├── normalised_PS.csv │ ├── normalised_PS_ctrls.csv │ └── raw_data │ │ ├── PS_comments.txt │ │ ├── PS_concentrations_reconstituted.csv │ │ ├── PS_draw_mean.csv │ │ ├── PS_draw_ratio.csv │ │ ├── PS_draw_std.csv │ │ ├── PS_everything.csv │ │ ├── PS_outliers.csv │ │ ├── PS_useful.csv │ │ ├── PS_yield_and_std.csv │ │ └── tecan_results.csv ├── data_active_learning │ ├── .ipynb_checkpoints │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── READme.md │ ├── all_duplicates_no_outliers.csv │ ├── all_duplicates_yields.csv │ ├── analysing_duplicates.ipynb │ ├── compare_al_plates.csv │ ├── duplicates │ │ ├── duplicated_plate_AL_1_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_2_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_3_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_3_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_8_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_8_plate_AL_9_yield.png │ │ └── duplicated_plate_AL_9_plate_AL_10_yield.png │ ├── duplicates_with_outliers │ │ ├── duplicated_plate_AL_1_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_2_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_3_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_1_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_3_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_2_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_4_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_3_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_5_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_4_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_6_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_5_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_7_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_6_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_8_yield.png │ │ ├── duplicated_plate_AL_7_plate_AL_9_yield.png │ │ ├── duplicated_plate_AL_8_plate_AL_10_yield.png │ │ ├── duplicated_plate_AL_8_plate_AL_9_yield.png │ │ └── duplicated_plate_AL_9_plate_AL_10_yield.png │ ├── extracting_duplicates.ipynb │ ├── plate_AL_10_useful.csv │ ├── plate_AL_1_useful.csv │ ├── plate_AL_2_useful.csv │ ├── plate_AL_3_useful.csv │ ├── plate_AL_4_useful.csv │ ├── plate_AL_5_useful.csv │ ├── plate_AL_6_useful.csv │ ├── plate_AL_7_useful.csv │ ├── plate_AL_8_useful.csv │ ├── plate_AL_9_useful.csv │ ├── raw_data │ │ ├── plate_AL_10_raw_everything.csv │ │ ├── plate_AL_1_raw_everything.csv │ │ ├── plate_AL_2_raw_everything.csv │ │ ├── plate_AL_3_raw_everything.csv │ │ ├── plate_AL_4_raw_everything.csv │ │ ├── plate_AL_5_raw_everything.csv │ │ ├── plate_AL_6_raw_everything.csv │ │ ├── plate_AL_7_raw_everything.csv │ │ ├── plate_AL_8_raw_everything.csv │ │ └── plate_AL_9_raw_everything.csv │ └── removed_example │ │ ├── duplicated_10_11_yield.png │ │ ├── duplicated_1_11_yield.png │ │ ├── duplicated_2_11_yield.png │ │ ├── duplicated_3_11_yield.png │ │ ├── duplicated_4_11_yield.png │ │ ├── duplicated_5_11_yield.png │ │ ├── duplicated_6_11_yield.png │ │ ├── duplicated_7_11_yield.png │ │ ├── duplicated_8_11_yield.png │ │ └── duplicated_9_11_yield.png ├── data_plate_ORI │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ ├── regression_AB_ORI_yieldreg_ref.png │ │ ├── regression_DH5_ORI_yieldreg_ref.png │ │ └── regression_PS_ORI_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_to_ORI.csv │ ├── duplicates │ │ ├── duplicated_AB_ORI_yield.png │ │ ├── duplicated_DH5_ORI_yield.png │ │ └── duplicated_PS_ORI_yield.png │ ├── extracting_duplicates.ipynb │ └── raw_data │ │ ├── AB_everything.csv │ │ ├── AB_intermediate_files │ │ ├── AB_comments.txt │ │ ├── AB_concentrations_reconstituted.csv │ │ ├── AB_draw_mean.csv │ │ ├── AB_draw_ratio.csv │ │ ├── AB_draw_std.csv │ │ ├── AB_outliers.csv │ │ └── AB_yield_and_std.csv │ │ ├── AB_useful.csv │ │ ├── DH5_everything.csv │ │ ├── DH5_intermediate_files │ │ ├── DH5_comments.txt │ │ ├── DH5_concentrations_reconstituted.csv │ │ ├── DH5_draw_mean.csv │ │ ├── DH5_draw_ratio.csv │ │ ├── DH5_draw_std.csv │ │ ├── DH5_outliers.csv │ │ └── DH5_yield_and_std.csv │ │ ├── DH5_useful.csv │ │ ├── ORI_everything.csv │ │ ├── ORI_intermediate_files │ │ ├── ORI_comments.txt │ │ ├── ORI_concentrations_reconstituted.csv │ │ ├── ORI_draw_mean.csv │ │ ├── ORI_draw_ratio.csv │ │ ├── ORI_draw_std.csv │ │ ├── ORI_outliers.csv │ │ └── ORI_yield_and_std.csv │ │ ├── ORI_useful.csv │ │ ├── PS_everything.csv │ │ ├── PS_intermediate_files │ │ ├── PS_comments.txt │ │ ├── PS_concentrations_reconstituted.csv │ │ ├── PS_draw_mean.csv │ │ ├── PS_draw_ratio.csv │ │ ├── PS_draw_std.csv │ │ ├── PS_outliers.csv │ │ └── PS_yield_and_std.csv │ │ ├── PS_useful.csv │ │ ├── compare_to_ORI.csv │ │ ├── concentrations_per_line │ │ ├── list_B_named_volumes_concentrations_reconstituted.csv │ │ ├── list_C_named_volumes_concentrations_reconstituted.csv │ │ ├── list_D_named_volumes_concentrations_reconstituted.csv │ │ ├── list_M_named_volumes_concentrations_reconstituted.csv │ │ ├── list_N_named_volumes_concentrations_reconstituted.csv │ │ └── list_O_named_volumes_concentrations_reconstituted.csv │ │ └── tecan_results.csv ├── data_plate_PS │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ ├── regression_double_DNA_to_PS_PS_to_PS_yieldreg_ref.png │ │ ├── regression_rifaxamin_to_PS_PS_to_PS_yieldreg_ref.png │ │ └── regression_spectinomycin_PS_PS_to_PS_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_to_PS.csv │ ├── duplicates │ │ ├── duplicated_double_DNA_to_PS_PS_to_PS_yield.png │ │ ├── duplicated_rifaxamin_to_PS_PS_to_PS_yield.png │ │ └── duplicated_spectinomycin_PS_PS_to_PS_yield.png │ ├── extracting_duplicates.ipynb │ └── raw_data │ │ ├── PS_everything.csv │ │ ├── PS_intermediate_files │ │ ├── PS_comments.txt │ │ ├── PS_concentrations_reconstituted.csv │ │ ├── PS_draw_mean.csv │ │ ├── PS_draw_ratio.csv │ │ ├── PS_draw_std.csv │ │ ├── PS_outliers.csv │ │ └── PS_yield_and_std.csv │ │ ├── PS_useful.csv │ │ ├── compare_to_PS.csv │ │ ├── double_DNA_everything.csv │ │ ├── double_DNA_intermediate_files │ │ ├── double_DNA_comments.txt │ │ ├── double_DNA_concentrations_reconstituted.csv │ │ ├── double_DNA_draw_mean.csv │ │ ├── double_DNA_draw_ratio.csv │ │ ├── double_DNA_draw_std.csv │ │ ├── double_DNA_outliers.csv │ │ └── double_DNA_yield_and_std.csv │ │ ├── double_DNA_useful.csv │ │ ├── rifaxamin │ │ ├── rifaxamin_comments.txt │ │ ├── rifaxamin_concentrations_reconstituted.csv │ │ ├── rifaxamin_draw_mean.csv │ │ ├── rifaxamin_draw_ratio.csv │ │ ├── rifaxamin_draw_std.csv │ │ ├── rifaxamin_outliers.csv │ │ └── rifaxamin_yield_and_std.csv │ │ ├── rifaxamin_everything.csv │ │ ├── rifaxamin_useful.csv │ │ ├── spectinomycin_everything.csv │ │ ├── spectinomycin_useful.csv │ │ ├── spectomycin │ │ ├── spectinomycin_comments.txt │ │ ├── spectinomycin_concentrations_reconstituted.csv │ │ ├── spectinomycin_draw_mean.csv │ │ ├── spectinomycin_draw_ratio.csv │ │ ├── spectinomycin_draw_std.csv │ │ ├── spectinomycin_outliers.csv │ │ └── spectinomycin_yield_and_std.csv │ │ └── tecan_results.csv ├── data_rifaxamin │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ └── regression_rifaxamin_rifaxamin_to_PS_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_rifaxamin.csv │ ├── duplicates │ │ └── duplicated_rifaxamin_rifaxamin_to_PS_yield.png │ ├── extracting_duplicates.ipynb │ ├── normalised_rifaxamin.csv │ └── raw_data │ │ ├── rifaxamin_comments.txt │ │ ├── rifaxamin_concentrations_reconstituted.csv │ │ ├── rifaxamin_draw_mean.csv │ │ ├── rifaxamin_draw_ratio.csv │ │ ├── rifaxamin_draw_std.csv │ │ ├── rifaxamin_everything.csv │ │ ├── rifaxamin_outliers.csv │ │ ├── rifaxamin_useful.csv │ │ ├── rifaxamin_yield_and_std.csv │ │ └── tecan_results.csv ├── data_spectinomycin │ ├── .ipynb_checkpoints │ │ ├── Extract_yield_own_autofluo-checkpoint.ipynb │ │ ├── analysing_duplicates-checkpoint.ipynb │ │ └── extracting_duplicates-checkpoint.ipynb │ ├── Extract_yield_own_autofluo.ipynb │ ├── all_duplicates_yields.csv │ ├── analyse_regressions │ │ └── regression_spectinomycin_spectinomycin_to_PS_yieldreg_ref.png │ ├── analysing_duplicates.ipynb │ ├── compare_spectinomycin.csv │ ├── duplicates │ │ └── duplicated_spectinomycin_spectinomycin_to_PS_yield.png │ ├── extracting_duplicates.ipynb │ ├── normalised_spectinomycin.csv │ └── raw_data │ │ ├── spectinomycin_comments.txt │ │ ├── spectinomycin_concentrations_reconstituted.csv │ │ ├── spectinomycin_draw_mean.csv │ │ ├── spectinomycin_draw_ratio.csv │ │ ├── spectinomycin_draw_std.csv │ │ ├── spectinomycin_everything.csv │ │ ├── spectinomycin_outliers.csv │ │ ├── spectinomycin_useful.csv │ │ ├── spectinomycin_yield_and_std.csv │ │ └── tecan_results.csv └── documentation.md ├── multiple_extracts_analysis ├── .ipynb_checkpoints │ ├── ID_n_informative_points-checkpoint.ipynb │ └── verify_informative_points-checkpoint.ipynb ├── AB │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── DH5_alpha │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── ID_n_informative_points.ipynb ├── ORI │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── showcase_1_model_vs_data.png │ ├── test.csv │ └── train.csv ├── PS │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── README.md ├── data │ ├── AB │ │ └── 102_points.csv │ ├── DH5_alpha │ │ └── 102_points.csv │ ├── ORI │ │ └── 102_points.csv │ ├── PS │ │ └── 102_points.csv │ ├── merged_data.csv │ ├── rifaximin │ │ └── 102_points.csv │ └── spectinomycin │ │ └── 102_points.csv ├── final_1.csv ├── rifaximin │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── spectinomycin │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv └── verify_informative_points.ipynb ├── predict_for_new_lysate ├── .ipynb_checkpoints │ ├── predict_extract_best_compositions-checkpoint.ipynb │ ├── predict_for_new_lysate-checkpoint.ipynb │ └── verify_informative_points-checkpoint.ipynb ├── AB │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── AB_10000.csv ├── AB_10000_exploitation.csv ├── AB_10000_exploration.csv ├── ORI │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── showcase_1_model_vs_data.png │ ├── test.csv │ └── train.csv ├── ORI_10000.csv ├── ORI_10000_exploitation.csv ├── ORI_10000_exploration.csv ├── PS │ ├── showcase_1.csv │ ├── showcase_1_model_vs_data.jpeg │ ├── test.csv │ └── train.csv ├── PS_10000.csv ├── PS_10000_exploitation.csv ├── PS_10000_exploration.csv ├── README.md ├── compare_10_best.csv ├── example_prediction_AB.csv ├── example_prediction_ORI.csv ├── example_prediction_PS.csv └── predict_for_new_lysate.ipynb └── whole_lysate_most_informative_points ├── .ipynb_checkpoints ├── ID_102_informative_points-checkpoint.ipynb ├── total_model_on_102-checkpoint.ipynb └── verify_informative_points-checkpoint.ipynb ├── 102_from_study ├── original_102_points.csv ├── showcase_1.csv ├── showcase_1_model_vs_data.jpeg ├── test.csv └── train.csv ├── 102_most_informative ├── final_1.csv ├── final_1_model_vs_data.png ├── final_2.csv ├── final_2_model_vs_data.png ├── final_3.csv ├── final_3_model_vs_data.png ├── final_4.csv ├── final_4_model_vs_data.png ├── final_5.csv ├── final_5_model_vs_data.png ├── iteration_0_1.csv ├── iteration_0_1_model_vs_data.png ├── iteration_2_1.csv ├── iteration_2_1_model_vs_data.png ├── iteration_2_2.csv ├── iteration_2_2_model_vs_data.png ├── iteration_2_3.csv ├── iteration_2_3_model_vs_data.png ├── iteration_4_1.csv ├── iteration_4_1_model_vs_data.png ├── iteration_4_2.csv ├── iteration_4_2_model_vs_data.png ├── iteration_4_3.csv ├── iteration_4_3_model_vs_data.png ├── iteration_4_4.csv ├── iteration_4_4_model_vs_data.png ├── iteration_4_5.csv ├── iteration_4_5_model_vs_data.png ├── iteration_6_1.csv ├── iteration_6_1_model_vs_data.png ├── iteration_6_2.csv ├── iteration_6_2_model_vs_data.png ├── iteration_6_3.csv ├── iteration_6_3_model_vs_data.png ├── iteration_6_4.csv ├── iteration_6_4_model_vs_data.png ├── iteration_6_5.csv ├── iteration_6_5_model_vs_data.png ├── iteration_8_1.csv ├── iteration_8_1_model_vs_data.png ├── iteration_8_2.csv ├── iteration_8_2_model_vs_data.png ├── iteration_8_3.csv ├── iteration_8_3_model_vs_data.png ├── iteration_8_4.csv ├── iteration_8_4_model_vs_data.png ├── iteration_8_5.csv └── iteration_8_5_model_vs_data.png ├── 102_most_informative_archive ├── final_1.csv ├── final_1_model_vs_data.jpeg ├── final_2.csv ├── final_2_model_vs_data.jpeg ├── final_3.csv ├── final_3_model_vs_data.jpeg ├── final_4.csv ├── final_4_model_vs_data.jpeg ├── final_5.csv ├── final_5_model_vs_data.jpeg ├── iteration_0_1.csv ├── iteration_0_1_model_vs_data.jpeg ├── iteration_2_1.csv ├── iteration_2_1_model_vs_data.jpeg ├── iteration_2_2.csv ├── iteration_2_2_model_vs_data.jpeg ├── iteration_2_3.csv ├── iteration_2_3_model_vs_data.jpeg ├── iteration_4_1.csv ├── iteration_4_1_model_vs_data.jpeg ├── iteration_4_2.csv ├── iteration_4_2_model_vs_data.jpeg ├── iteration_4_3.csv ├── iteration_4_3_model_vs_data.jpeg ├── iteration_4_4.csv ├── iteration_4_4_model_vs_data.jpeg ├── iteration_4_5.csv ├── iteration_4_5_model_vs_data.jpeg ├── iteration_6_1.csv ├── iteration_6_1_model_vs_data.jpeg ├── iteration_6_2.csv ├── iteration_6_2_model_vs_data.jpeg ├── iteration_6_3.csv ├── iteration_6_3_model_vs_data.jpeg ├── iteration_6_4.csv ├── iteration_6_4_model_vs_data.jpeg ├── iteration_6_5.csv ├── iteration_6_5_model_vs_data.jpeg ├── iteration_8_1.csv ├── iteration_8_1_model_vs_data.jpeg ├── iteration_8_2.csv ├── iteration_8_2_model_vs_data.jpeg ├── iteration_8_3.csv ├── iteration_8_3_model_vs_data.jpeg ├── iteration_8_4.csv ├── iteration_8_4_model_vs_data.jpeg ├── iteration_8_5.csv └── iteration_8_5_model_vs_data.jpeg ├── 20_most_informative ├── original_20_points.csv ├── showcase_1.csv ├── showcase_1_model_vs_data.jpeg ├── test.csv └── train.csv ├── ID_102_informative_points.ipynb ├── README.md ├── data ├── no_controls │ ├── plate_AL_10_raw_yield_and_std.csv │ ├── plate_AL_1_raw_yield_and_std.csv │ ├── plate_AL_2_raw_yield_and_std.csv │ ├── plate_AL_3_raw_yield_and_std.csv │ ├── plate_AL_4_raw_yield_and_std.csv │ ├── plate_AL_5_raw_yield_and_std.csv │ ├── plate_AL_6_raw_yield_and_std.csv │ ├── plate_AL_7_raw_yield_and_std.csv │ ├── plate_AL_8_raw_yield_and_std.csv │ └── plate_AL_9_raw_yield_and_std.csv ├── plate_AL_10_raw_everything.csv ├── plate_AL_1_raw_everything.csv ├── plate_AL_2_raw_everything.csv ├── plate_AL_3_raw_everything.csv ├── plate_AL_4_raw_everything.csv ├── plate_AL_5_raw_everything.csv ├── plate_AL_6_raw_everything.csv ├── plate_AL_7_raw_everything.csv ├── plate_AL_8_raw_everything.csv └── plate_AL_9_raw_everything.csv ├── full_on_102 ├── excepted_test.csv ├── full_on_102_1.csv ├── full_on_102_1_model_vs_data.jpeg ├── full_on_102_1_model_vs_data_test.jpeg ├── test.csv └── train.csv ├── full_on_102_bis ├── full_on_102_1.csv ├── full_on_102_1_model_vs_data.png ├── full_on_102_1_model_vs_data_test.png ├── test.csv └── train.csv ├── merged_data_and_model.csv ├── total_model_on_102.ipynb └── verify_informative_points.ipynb /ECHO_handling_scripts/example/concentrations_line_A.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter 2 | 0.033,0.0068,50,0.026,10,2,0.15,0.1,3,0.15,0.02,0.4,50,0.075,8,10 3 | 0.165,0.0068,50,0.026,10,2,0.15,0.1,9,0.15,0.02,0.4,50,0.375,24,10 4 | 0.099,0.0204,50,0.078,10,2,0.15,0.5,3,0.45,0.1,1.2,50,0.225,8,10 5 | 0.033,0.0204,50,0.078,10,2,0.15,0.5,9,0.45,0.06,2,50,0.225,24,10 6 | 0.33,0.068,0,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,80,10 7 | 0.33,0.068,50,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,80,10 8 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/concentrations_line_A_completed.csv: -------------------------------------------------------------------------------- 1 | #extract;mg_gluta;K_gluta;aa;peg;hepes;trna;coa;nad;camp;folinic_acid;spermidin;pga;nucleo_mix;DNA;promoter;RBS 2 | 30;0.4;8;0.15;2;50;0.02;0.026;0.033;0.075;0.0068;0.1;3;0.15;50;10;10 3 | 30;0.4;24;0.15;2;50;0.02;0.026;0.165;0.375;0.0068;0.1;9;0.15;50;10;10 4 | 30;1.2;8;0.45;2;50;0.1;0.078;0.099;0.225;0.0204;0.5;3;0.15;50;10;10 5 | 30;2;24;0.45;2;50;0.06;0.078;0.033;0.225;0.0204;0.5;9;0.15;50;10;10 6 | 30;4;80;1.5;2;50;0.2;0.26;0.33;0.75;0.068;1;30;1.5;0;10;10 7 | 30;4;80;1.5;2;50;0.2;0.26;0.33;0.75;0.068;1;30;1.5;50;10;10 8 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/concentrations_line_P.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter 2 | 0.165,0.034,50,0.026,10,2,0.75,0.5,15,0.45,0.02,2,50,0.225,40,10 3 | 0.099,0.034,50,0.026,10,2,0.75,0.3,15,0.75,0.02,1.2,50,0.375,40,10 4 | 0.165,0.0204,50,0.078,10,2,0.75,0.5,9,0.15,0.02,0.4,50,0.375,40,10 5 | 0.033,0.0068,50,0.026,10,2,0.75,0.3,15,0.75,0.02,2,50,0.375,24,10 6 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,80,10 7 | 0.099,0.034,50,0.026,10,2,1.5,0.1,9,1.5,0.1,4,50,0.075,80,10 8 | 0.033,0.0204,50,0.078,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,80,10 9 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/concentrations_line_P_completed.csv: -------------------------------------------------------------------------------- 1 | #extract;mg_gluta;K_gluta;aa;peg;hepes;trna;coa;nad;camp;folinic_acid;spermidin;pga;nucleo_mix;DNA;promoter;RBS 2 | 30;2;40;0.45;2;50;0.02;0.026;0.165;0.225;0.034;0.5;15;0.75;50;10;10 3 | 30;1.2;40;0.75;2;50;0.02;0.026;0.099;0.375;0.034;0.3;15;0.75;50;10;10 4 | 30;0.4;40;0.15;2;50;0.02;0.078;0.165;0.375;0.0204;0.5;9;0.75;50;10;10 5 | 30;2;24;0.75;2;50;0.02;0.026;0.033;0.375;0.0068;0.3;15;0.75;50;10;10 6 | 30;4;80;1.5;2;50;0.06;0.026;0.165;0.075;0.068;0.1;9;1.5;50;10;10 7 | 30;4;80;1.5;2;50;0.1;0.026;0.099;0.075;0.034;0.1;9;1.5;50;10;10 8 | 30;4;80;1.5;2;50;0.06;0.078;0.033;0.075;0.0204;0.1;9;1.5;50;10;10 9 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/example_aa.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,2.6,2.6,0,0,0,0,2.6,2.6,0,0,0,0,2.6,2.6,0,0,0,0 3 | B,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 4 | C,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 5 | D,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 6 | E,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 7 | F,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 8 | G,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 9 | H,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 10 | I,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 11 | J,0,1.3,1.3,1.3,0,0,0,0,0,0,0,0,0,0,0,0,1.3,1.3,1.3,1.3,1.3,1.3 12 | K,0,0,0,0,0,0,1.3,1.3,1.3,0,0,0,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3 13 | L,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,2.6,2.6,2.6,2.6,2.6 14 | M,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6 15 | N,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6 16 | O,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,0,0 17 | P,0,1.3,0,1.3,2.6,2.6,2.6,0,1.3,0,1.3,2.6,2.6,2.6,0,1.3,0,1.3,2.6,2.6,2.6,0 18 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/example_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 115 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /ECHO_handling_scripts/example/example_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/concentrations_line_A.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter 2 | 0.033,0.0068,50,0.026,10,2,0.15,0.1,3,0.15,0.02,0.4,50,0.075,4,10 3 | 0.165,0.0068,50,0.026,10,2,0.15,0.1,9,0.15,0.02,0.4,50,0.375,12,10 4 | 0.099,0.0204,50,0.078,10,2,0.15,0.5,3,0.45,0.1,1.2,50,0.225,4,10 5 | 0.033,0.0204,50,0.078,10,2,0.15,0.5,9,0.45,0.06,2,50,0.225,12,10 6 | 0.33,0.068,0,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10 7 | 0.33,0.068,50,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10 8 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/concentrations_line_A_completed.csv: -------------------------------------------------------------------------------- 1 | #extract;mg_gluta;K_gluta;aa;peg;hepes;trna;coa;nad;camp;folinic_acid;spermidin;pga;nucleo_mix;DNA;promoter;RBS 2 | 30;0.4;4;0.15;2;50;0.02;0.026;0.033;0.075;0.0068;0.1;3;0.15;50;10;10 3 | 30;0.4;12;0.15;2;50;0.02;0.026;0.165;0.375;0.0068;0.1;9;0.15;50;10;10 4 | 30;1.2;4;0.45;2;50;0.1;0.078;0.099;0.225;0.0204;0.5;3;0.15;50;10;10 5 | 30;2;12;0.45;2;50;0.06;0.078;0.033;0.225;0.0204;0.5;9;0.15;50;10;10 6 | 30;4;40;1.5;2;50;0.2;0.26;0.33;0.75;0.068;1;30;1.5;0;10;10 7 | 30;4;40;1.5;2;50;0.2;0.26;0.33;0.75;0.068;1;30;1.5;50;10;10 8 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/concentrations_line_P.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter 2 | 0.165,0.034,50,0.026,10,2,0.75,0.5,15,0.45,0.02,2,50,0.225,20,10 3 | 0.099,0.034,50,0.026,10,2,0.75,0.3,15,0.75,0.02,1.2,50,0.375,20,10 4 | 0.165,0.0204,50,0.078,10,2,0.75,0.5,9,0.15,0.02,0.4,50,0.375,20,10 5 | 0.033,0.0068,50,0.026,10,2,0.75,0.3,15,0.75,0.02,2,50,0.375,12,10 6 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10 7 | 0.099,0.034,50,0.026,10,2,1.5,0.1,9,1.5,0.1,4,50,0.075,40,10 8 | 0.033,0.0204,50,0.078,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10 9 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/concentrations_line_P_completed.csv: -------------------------------------------------------------------------------- 1 | #extract;mg_gluta;K_gluta;aa;peg;hepes;trna;coa;nad;camp;folinic_acid;spermidin;pga;nucleo_mix;DNA;promoter;RBS 2 | 30;2;20;0.45;2;50;0.02;0.026;0.165;0.225;0.034;0.5;15;0.75;50;10;10 3 | 30;1.2;20;0.75;2;50;0.02;0.026;0.099;0.375;0.034;0.3;15;0.75;50;10;10 4 | 30;0.4;20;0.15;2;50;0.02;0.078;0.165;0.375;0.0204;0.5;9;0.75;50;10;10 5 | 30;2;12;0.75;2;50;0.02;0.026;0.033;0.375;0.0068;0.3;15;0.75;50;10;10 6 | 30;4;40;1.5;2;50;0.06;0.026;0.165;0.075;0.068;0.1;9;1.5;50;10;10 7 | 30;4;40;1.5;2;50;0.1;0.026;0.099;0.075;0.034;0.1;9;1.5;50;10;10 8 | 30;4;40;1.5;2;50;0.06;0.078;0.033;0.075;0.0204;0.1;9;1.5;50;10;10 9 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/example_aa.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,2.6,2.6,0,0,0,0,2.6,2.6,0,0,0,0,2.6,2.6,0,0,0,0 3 | B,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 4 | C,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 5 | D,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 6 | E,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 7 | F,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 8 | G,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 9 | H,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 10 | I,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 11 | J,0,1.3,1.3,1.3,0,0,0,0,0,0,0,0,0,0,0,0,1.3,1.3,1.3,1.3,1.3,1.3 12 | K,0,0,0,0,0,0,1.3,1.3,1.3,0,0,0,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3 13 | L,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,1.3,2.6,2.6,2.6,2.6,2.6 14 | M,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6 15 | N,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6 16 | O,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,2.6,0,0 17 | P,0,1.3,0,1.3,2.6,2.6,2.6,0,1.3,0,1.3,2.6,2.6,2.6,0,1.3,0,1.3,2.6,2.6,2.6,0 18 | -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/example_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 115 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /ECHO_handling_scripts/example_original/example_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /active_learning_loop/README.md: -------------------------------------------------------------------------------- 1 | # Description. 2 | 3 | This folder contains all data and scripts to generate data presented in Figures 1c,d and e of the paper Large scale active-learning-guided exploration to maximize cell-free production. 4 | 5 | # Data: 6 | 7 | Contains the whole data from this study. 8 | data/no_controls contains data from rows B to O, without controls from lines A and P. 9 | 10 | # Figure 1.c: initial training set 11 | 12 | The code to generate the initial training set is 13 | 14 | 15 | # Figure 1.d: active learning loop 16 | 17 | The script to generate the active leaning loop is learn_and_suggest. 18 | 19 | # Figure 1e: model statistics 20 | 21 | The script to generate the 5 fold cross validation. 22 | -------------------------------------------------------------------------------- /active_learning_loop/model_statistics/iteration_10fold_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/active_learning_loop/model_statistics/iteration_10fold_1.png -------------------------------------------------------------------------------- /active_learning_loop/model_statistics/iteration_10fold_2.png: -------------------------------------------------------------------------------- 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8,0.904692695551282,0.017665933922977373 10 | 9,0.9193921115982896,0.010557763188460776 11 | 10,0.9199610668175122,0.011078690089110662 12 | -------------------------------------------------------------------------------- /compounds_effect_analysis/AB/coefficents_from_lin_reg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/AB/coefficents_from_lin_reg.png -------------------------------------------------------------------------------- /compounds_effect_analysis/AB/coefficents_from_lin_reg_intercept.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/AB/coefficents_from_lin_reg_intercept.png 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folinic_acid,[0.04477397] 4 | coa,[0] 5 | nucleo_mix,[0.37353105] 6 | spermidin,[0.41520416] 7 | pga,[0.36144257] 8 | aa,[0.5604086] 9 | trna,[0.0923644] 10 | mg_gluta,[0.4186871] 11 | camp,[0.06976707] 12 | K_gluta,[0.38452473] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/AB_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/AB_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/DH5_alpha/coefficents_from_lin_reg.png: -------------------------------------------------------------------------------- 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coa,-0.045780505342596325,0.034486017101081366 5 | nucleo_mix,-0.2989655570958724,0.10743876921872213 6 | spermidin,-0.8161624408266676,0.015356380392741072 7 | pga,0.016267326973937783,0.08396526380419729 8 | aa,-0.24520779035300871,0.01343547837989674 9 | trna,-0.07517881549728958,0.03642452975584194 10 | mg_gluta,-0.04637976429703722,0.07739584238897819 11 | camp,-0.15877499246473314,0.08280661644854084 12 | K_gluta,0.5084838601663026,0.13150289455748082 13 | intercept,1.249259799434531,0.018778419386069483 14 | -------------------------------------------------------------------------------- /compounds_effect_analysis/DH5_alpha/lin_reg_fold_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/DH5_alpha/lin_reg_fold_1.png -------------------------------------------------------------------------------- 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12 | K_gluta,[0.28037522] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/DH5_alpha_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/DH5_alpha_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI/coefficents_from_lin_reg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/ORI/coefficents_from_lin_reg.png -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI/coefficents_from_lin_reg_intercept.png: 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camp,-0.4907852792340188,0.2503720819201278 12 | K_gluta,1.4668304924396103,0.44166705355363534 13 | intercept,1.2386631901144085,0.20543838983119708 14 | -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI/lin_reg_fold_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/ORI/lin_reg_fold_1.png -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI/lin_reg_fold_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/ORI/lin_reg_fold_2.png -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /compounds_effect_analysis/ORI_full/coefficents_from_linear.csv: -------------------------------------------------------------------------------- 1 | Name,Mean,Std 2 | nad,-0.02420751811898144,0.011382413459825458 3 | folinic_acid,-0.03653995326491176,0.024791103148131672 4 | coa,-0.23610891700147224,0.01849146718221555 5 | nucleo_mix,0.5443085848538054,0.11106823923711379 6 | spermidin,-1.3775742378283098,0.013675454786433899 7 | pga,-0.5362494464397611,0.05335606756094268 8 | aa,0.5151688937917402,0.024199897936613483 9 | trna,-0.06872883957966641,0.020650255402772225 10 | mg_gluta,0.4328088796468048,0.03682421820666637 11 | camp,-0.34916294448531454,0.07439435001163937 12 | K_gluta,0.6937058721206526,0.08459701637083487 13 | intercept,0.6929138669231285,0.028450373260775392 14 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /compounds_effect_analysis/ORI_full_mi/coefficents_from_mi.csv: -------------------------------------------------------------------------------- 1 | Name,Mean 2 | nad,[0.07946158] 3 | folinic_acid,[0.08228938] 4 | coa,[0.09227163] 5 | nucleo_mix,[0.60488321] 6 | spermidin,[0.35587828] 7 | pga,[0.44254968] 8 | aa,[0.38736416] 9 | trna,[0.0670929] 10 | mg_gluta,[0.55226844] 11 | camp,[0.11397836] 12 | K_gluta,[0.63999157] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI_full_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/ORI_full_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI_mi/coefficents_from_mi.csv: -------------------------------------------------------------------------------- 1 | Name,Mean 2 | nad,[0] 3 | folinic_acid,[0.02623669] 4 | coa,[0.03275248] 5 | nucleo_mix,[0.69475605] 6 | spermidin,[0.40642426] 7 | pga,[0.43022609] 8 | aa,[0.28804205] 9 | trna,[0.00379209] 10 | mg_gluta,[0.66387156] 11 | camp,[0.15815189] 12 | K_gluta,[0.75121942] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/ORI_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/ORI_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/PS/coefficents_from_lin_reg.png: 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4 | coa,-0.2639123050787321,0.11623824986554465 5 | nucleo_mix,-0.4353105627997005,0.4846186980362682 6 | spermidin,-1.6248861265009036,0.0632672963608214 7 | pga,-1.0355851330353585,0.36109786805158045 8 | aa,0.4380589653869545,0.027749178426989582 9 | trna,-0.14590978133507987,0.041642238899824095 10 | mg_gluta,0.6509183827042022,0.17064926922271884 11 | camp,-0.34568147813907313,0.08233254073597039 12 | K_gluta,0.9684895111201157,0.30093569973237205 13 | intercept,1.1130049958795754,0.22570639165631906 14 | -------------------------------------------------------------------------------- /compounds_effect_analysis/PS/lin_reg_fold_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/PS/lin_reg_fold_1.png -------------------------------------------------------------------------------- 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| -------------------------------------------------------------------------------- /compounds_effect_analysis/PS_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/PS_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/README.md: -------------------------------------------------------------------------------- 1 | # Description: 2 | 3 | This folder contains experimental data from OB, PS and AB. 4 | 5 | The linear_analysis notebook allows running a linear regression and extracting the coefficients caracterising the lysate. 6 | 7 | The mutual_information_analysis notebook allows for running mutual information analysis and extracting those coefficients (Figure 1c, Supplementary Figure 3) 8 | 9 | 10 | 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-------------------------------------------------------------------------------- 1 | Name,Mean,Std 2 | nad,0.2792550477768846,0.025240157794132252 3 | folinic_acid,0.05190921318864798,0.015531185974577687 4 | coa,-0.4215403121276231,0.15721143450978173 5 | nucleo_mix,-0.13426716785127918,0.44764448438466126 6 | spermidin,-1.6967745371418637,0.048579641234023654 7 | pga,-1.7084471170055846,0.21925304834226114 8 | aa,0.8267792939567051,0.05539127806460182 9 | trna,0.07737007595688442,0.03003727378392695 10 | mg_gluta,0.43615375073060847,0.16216696614489656 11 | camp,-0.209635128559988,0.1420509330400677 12 | K_gluta,0.48225742277581396,0.25687798425319563 13 | intercept,2.0059700213405747,0.15121039994346822 14 | -------------------------------------------------------------------------------- /compounds_effect_analysis/rifaximin/lin_reg_fold_1.png: -------------------------------------------------------------------------------- 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Name,Mean 2 | nad,[0.07139663] 3 | folinic_acid,[0] 4 | coa,[0.01706666] 5 | nucleo_mix,[0.40768069] 6 | spermidin,[0.53953728] 7 | pga,[0.34012879] 8 | aa,[0.42714122] 9 | trna,[0.06547211] 10 | mg_gluta,[0.35835521] 11 | camp,[0.15428651] 12 | K_gluta,[0.41192731] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/rifaximin_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/rifaximin_mi/mutual_information.png -------------------------------------------------------------------------------- /compounds_effect_analysis/spectinomycin/coefficents_from_lin_reg.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/spectinomycin/coefficents_from_lin_reg.png -------------------------------------------------------------------------------- /compounds_effect_analysis/spectinomycin/coefficents_from_lin_reg_intercept.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/spectinomycin/coefficents_from_lin_reg_intercept.png -------------------------------------------------------------------------------- /compounds_effect_analysis/spectinomycin/coefficents_from_linear.csv: -------------------------------------------------------------------------------- 1 | Name,Mean,Std 2 | nad,-0.18057478476627403,0.027198868342561355 3 | folinic_acid,0.028947012036605636,0.06162926842678389 4 | coa,-0.19603160739763584,0.03862452846450071 5 | nucleo_mix,-0.0727542085453959,0.28243074600958734 6 | spermidin,-0.957777174418171,0.028309003812579947 7 | pga,-0.27687659466788556,0.1234914837121386 8 | aa,-0.0726123929111459,0.055692108541829204 9 | trna,-0.0483834026812922,0.022534245121376865 10 | mg_gluta,0.2527472915964048,0.12620688735899308 11 | camp,-0.29012577368121917,0.06804984326760258 12 | K_gluta,0.1645937214023442,0.18925712374147988 13 | intercept,1.4631861928223093,0.04435907653783632 14 | -------------------------------------------------------------------------------- /compounds_effect_analysis/spectinomycin/lin_reg_fold_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/spectinomycin/lin_reg_fold_1.png -------------------------------------------------------------------------------- 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mg_gluta,[0.23737225] 11 | camp,[0.03316965] 12 | K_gluta,[0.31708127] 13 | -------------------------------------------------------------------------------- /compounds_effect_analysis/spectinomycin_mi/mutual_information.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/compounds_effect_analysis/spectinomycin_mi/mutual_information.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_AB/analyse_regressions/regression_AB_AB_to_ORI_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_AB/analyse_regressions/regression_AB_AB_to_ORI_yieldreg_ref.png 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0.165,0.0204,50.0,0.078,10.0,2.0,0.75,0.5,9.0,0.15,0.02,0.4,50.0,0.375,20.0,10.0,19438.0,10053.0,8696.0,AB 3 | 0.033,0.0068,50.0,0.026,10.0,2.0,0.75,0.3,15.0,0.75,0.02,2.0,50.0,0.375,12.0,10.0,25715.0,13504.0,12923.0,AB 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_DH5_alpha/analyse_regressions/regression_DH5_DH5_to_ORI_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_DH5_alpha/analyse_regressions/regression_DH5_DH5_to_ORI_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_DH5_alpha/analyse_regressions/regression_DH5_to_ORI_DH5_yieldreg_ref.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /controls_analysis_plates/data_active_learning/READme.md: -------------------------------------------------------------------------------- 1 | This folder contains data for the Active Learning loop presented in... 2 | 3 | Outliers removal: 4 | 5 | Some points are visibly outliers as can be seen in du)plication figures in duplicates_with_outliers folders. 6 | 7 | Some points were therefore removed for R2 calculations. 8 | 9 | Removed points: 10 | P4 is a problem but it's unclear where. 11 | 10, 6 12 | 10, 5 13 | 6, 4 14 | 15 | P2: 10, 4 16 | 17 | P4 is extremely unstable (seems to have 2 mode,s 0.2 or 0.6) 18 | 19 | D9, P6 (4, 6) 20 | D9, P6 (4, 5) 21 | 22 | 3 et 10: rien ne va. P4, P5?, A4, A2 23 | 3 et 9: rien ne va. P4, P5?, A4, A2 24 | 25 | 2 et 10 (9, 8?) 26 | P4, P2 27 | 28 | 29 | Remove P4 everywhere. 30 | Plate 3: remove A4 et A2. 31 | 32 | See what that give sme. 33 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_active_learning/duplicates/duplicated_plate_AL_1_plate_AL_10_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_active_learning/duplicates/duplicated_plate_AL_1_plate_AL_10_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_active_learning/duplicates/duplicated_plate_AL_1_plate_AL_2_yield.png: -------------------------------------------------------------------------------- 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https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_ORI/duplicates/duplicated_PS_ORI_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,11836.7,12597.3,10725.7,8248.7,4382.0,5081.7,11836.7,12597.3,10725.7,8248.7,4382.0,5081.7,11836.7,12597.3,10725.7,8248.7,4382.0,5081.7,0,0,0,0 4 | N,13609.7,13520.0,12145.3,16154.0,42921.3,42928.3,42240.7,13609.7,13520.0,12145.3,16154.0,42921.3,42928.3,42240.7,13609.7,13520.0,12145.3,16154.0,42921.3,42928.3,42240.7,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,7.638953424518657,4.650996642137601,1.7537316911716716,0.4230969728563288,0.670926517571885,2.7451443414605348,7.638953424518657,4.650996642137601,1.7537316911716716,0.4230969728563288,0.670926517571885,2.7451443414605348,7.638953424518657,4.650996642137601,1.7537316911716716,0.4230969728563288,0.670926517571885,2.7451443414605348,0,0,0,0 4 | N,3.9258763969815638,7.021449704142012,10.19324347690053,6.288844868144112,6.045017275804787,3.0436798102883174,5.43764662990907,3.9258763969815638,7.021449704142012,10.19324347690053,6.288844868144112,6.045017275804787,3.0436798102883174,5.43764662990907,3.9258763969815638,7.021449704142012,10.19324347690053,6.288844868144112,6.045017275804787,3.0436798102883174,5.43764662990907,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,904.2,585.9,188.1,34.9,29.4,139.5,904.2,585.9,188.1,34.9,29.4,139.5,904.2,585.9,188.1,34.9,29.4,139.5,0,0,0,0 4 | N,534.3,949.3,1238.0,1015.9,2594.6,1306.6,2296.9,534.3,949.3,1238.0,1015.9,2594.6,1306.6,2296.9,534.3,949.3,1238.0,1015.9,2594.6,1306.6,2296.9,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_intermediate_files/AB_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.372,0.0451 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.4099,0.0292 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.3165,0.0094 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.1929,0.0017 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.0349,0.007 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,0.4605,0.0267 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,0.456,0.0474 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.3874,0.0618 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,0.5874,0.0507 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,1.9231,0.1295 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,1.9234,0.0652 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,1.8891,0.1146 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/AB_useful.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,yield_std,plaque_name,well_1 2 | 0.033,0.0068,50,0.026,10,2,0.15,0.1,3,0.15,0.02,0.4,50,0.075,4,10,0.372,0.0451,AB,C2 3 | 0.165,0.0068,50,0.026,10,2,0.15,0.1,9,0.15,0.02,0.4,50,0.375,12,10,0.4099,0.0292,AB,C3 4 | 0.099,0.0204,50,0.078,10,2,0.15,0.5,3,0.45,0.1,1.2,50,0.225,4,10,0.3165,0.0094,AB,C4 5 | 0.033,0.0204,50,0.078,10,2,0.15,0.5,9,0.45,0.06,2,50,0.225,12,10,0.1929,0.0017,AB,C5 6 | 0.33,0.068,0,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0,0.0015,AB,C6 7 | 0.33,0.068,50,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0.0349,0.007,AB,C7 8 | 0.165,0.034,50,0.026,10,2,0.75,0.5,15,0.45,0.02,2,50,0.225,20,10,0.4605,0.0267,AB,N2 9 | 0.099,0.034,50,0.026,10,2,0.75,0.3,15,0.75,0.02,1.2,50,0.375,20,10,0.456,0.0474,AB,N3 10 | 0.165,0.0204,50,0.078,10,2,0.75,0.5,9,0.15,0.02,0.4,50,0.375,20,10,0.3874,0.0618,AB,N4 11 | 0.033,0.0068,50,0.026,10,2,0.75,0.3,15,0.75,0.02,2,50,0.375,12,10,0.5874,0.0507,AB,N5 12 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,1.9231,0.1295,AB,N6 13 | 0.099,0.034,50,0.026,10,2,1.5,0.1,9,1.5,0.1,4,50,0.075,40,10,1.9234,0.0652,AB,N7 14 | 0.033,0.0204,50,0.078,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,1.8891,0.1146,AB,N8 15 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,21184.7,27952.0,19317.3,21399.3,4392.7,10405.0,21184.7,27952.0,19317.3,21399.3,4392.7,10405.0,21184.7,27952.0,19317.3,21399.3,4392.7,10405.0,0,0,0,0 4 | M,38240.0,41328.0,40206.7,43770.7,36441.7,38774.0,42043.3,38240.0,41328.0,40206.7,43770.7,36441.7,38774.0,42043.3,38240.0,41328.0,40206.7,43770.7,36441.7,38774.0,42043.3,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,3.2627320660665484,5.191399542072124,4.14136551174336,2.6141041996700825,5.912081407790197,4.098029793368572,3.2627320660665484,5.191399542072124,4.14136551174336,2.6141041996700825,5.912081407790197,4.098029793368572,3.2627320660665484,5.191399542072124,4.14136551174336,2.6141041996700825,5.912081407790197,4.098029793368572,0,0,0,0 4 | M,5.451882845188285,4.693186217576462,9.486229906955806,2.593287290356334,5.066174190556424,2.331459225254036,5.35210128605509,5.451882845188285,4.693186217576462,9.486229906955806,2.593287290356334,5.066174190556424,2.331459225254036,5.35210128605509,5.451882845188285,4.693186217576462,9.486229906955806,2.593287290356334,5.066174190556424,2.331459225254036,5.35210128605509,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,691.2,1451.1,800.0,559.4,259.7,426.4,691.2,1451.1,800.0,559.4,259.7,426.4,691.2,1451.1,800.0,559.4,259.7,426.4,0,0,0,0 4 | M,2084.8,1939.6,3814.1,1135.1,1846.2,904.0,2250.2,2084.8,1939.6,3814.1,1135.1,1846.2,904.0,2250.2,2084.8,1939.6,3814.1,1135.1,1846.2,904.0,2250.2,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/DH5_intermediate_files/DH5_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.8384,0.0345 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,1.1762,0.0724 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.7451,0.0399 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.8491,0.0279 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.3002,0.0213 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,1.6899,0.1041 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,1.844,0.0968 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,1.788,0.1904 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,1.966,0.0567 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,1.6001,0.0922 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,1.7165,0.0451 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,1.8797,0.1123 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,17664.0,11648.0,14171.7,10879.3,4898.7,5794.7,17664.0,11648.0,14171.7,10879.3,4898.7,5794.7,17664.0,11648.0,14171.7,10879.3,4898.7,5794.7,0,0,0,0 3 | P,22661.3,24422.3,22571.3,25647.3,46447.0,44144.3,42934.0,22661.3,24422.3,22571.3,25647.3,46447.0,44144.3,42934.0,22661.3,24422.3,22571.3,25647.3,46447.0,44144.3,42934.0,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,1.8478260869565215,0.9933035714285714,2.062561301749261,1.6094785510097156,2.5169943046114276,1.7343434517748977,1.8478260869565215,0.9933035714285714,2.062561301749261,1.6094785510097156,2.5169943046114276,1.7343434517748977,1.8478260869565215,0.9933035714285714,2.062561301749261,1.6094785510097156,2.5169943046114276,1.7343434517748977,0,0,0,0 3 | P,0.4452524788957386,3.0705543703909948,5.291232671578508,4.0218658494266455,5.219712790922988,6.528136135356094,13.322075744165463,0.4452524788957386,3.0705543703909948,5.291232671578508,4.0218658494266455,5.219712790922988,6.528136135356094,13.322075744165463,0.4452524788957386,3.0705543703909948,5.291232671578508,4.0218658494266455,5.219712790922988,6.528136135356094,13.322075744165463,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,326.4,115.7,292.3,175.1,123.3,100.5,326.4,115.7,292.3,175.1,123.3,100.5,326.4,115.7,292.3,175.1,123.3,100.5,0,0,0,0 3 | P,100.9,749.9,1194.3,1031.5,2424.4,2881.8,5719.7,100.9,749.9,1194.3,1031.5,2424.4,2881.8,5719.7,100.9,749.9,1194.3,1031.5,2424.4,2881.8,5719.7,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_intermediate_files/ORI_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.6538,0.0167 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.3457,0.0059 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.475,0.015 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.3063,0.009 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.0459,0.0051 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,0.9098,0.0052 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,1.0,0.0384 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.9052,0.0612 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,1.0627,0.0528 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,2.1281,0.1242 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,2.0102,0.1476 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,1.9482,0.293 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/ORI_useful.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,yield_std,plaque_name,well_1 2 | 0.033,0.0068,50,0.026,10,2,0.15,0.1,3,0.15,0.02,0.4,50,0.075,4,10,0.6538,0.0167,ORI,A2 3 | 0.165,0.0068,50,0.026,10,2,0.15,0.1,9,0.15,0.02,0.4,50,0.375,12,10,0.3457,0.0059,ORI,A3 4 | 0.099,0.0204,50,0.078,10,2,0.15,0.5,3,0.45,0.1,1.2,50,0.225,4,10,0.475,0.015,ORI,A4 5 | 0.033,0.0204,50,0.078,10,2,0.15,0.5,9,0.45,0.06,2,50,0.225,12,10,0.3063,0.009,ORI,A5 6 | 0.33,0.068,0,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0,0.0063,ORI,A6 7 | 0.33,0.068,50,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0.0459,0.0051,ORI,A7 8 | 0.165,0.034,50,0.026,10,2,0.75,0.5,15,0.45,0.02,2,50,0.225,20,10,0.9098,0.0052,ORI,P2 9 | 0.099,0.034,50,0.026,10,2,0.75,0.3,15,0.75,0.02,1.2,50,0.375,20,10,1,0.0384,ORI,P3 10 | 0.165,0.0204,50,0.078,10,2,0.75,0.5,9,0.15,0.02,0.4,50,0.375,20,10,0.9052,0.0612,ORI,P4 11 | 0.033,0.0068,50,0.026,10,2,0.75,0.3,15,0.75,0.02,2,50,0.375,12,10,1.0627,0.0528,ORI,P5 12 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,2.1281,0.1242,ORI,P6 13 | 0.099,0.034,50,0.026,10,2,1.5,0.1,9,1.5,0.1,4,50,0.075,40,10,2.0102,0.1476,ORI,P7 14 | 0.033,0.0204,50,0.078,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,1.9482,0.293,ORI,P8 15 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,16973.0,13691.0,12442.7,9038.0,3863.7,5836.0,16973.0,13691.0,12442.7,9038.0,3863.7,5836.0,16973.0,13691.0,12442.7,9038.0,3863.7,5836.0,0,0,0,0 4 | O,25488.7,25362.3,17443.3,27912.3,63083.3,60528.7,62058.7,25488.7,25362.3,17443.3,27912.3,63083.3,60528.7,62058.7,25488.7,25362.3,17443.3,27912.3,63083.3,60528.7,62058.7,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,3.592764979673599,4.395588342706888,4.82612294759176,0.36401858818322635,1.9489090767916766,4.374571624400274,3.592764979673599,4.395588342706888,4.82612294759176,0.36401858818322635,1.9489090767916766,4.374571624400274,3.592764979673599,4.395588342706888,4.82612294759176,0.36401858818322635,1.9489090767916766,4.374571624400274,0,0,0,0 4 | O,6.86264893854924,7.943680186733854,10.354692059415363,10.354216599850245,2.8598694107632285,1.8842301255437504,6.005765509106701,6.86264893854924,7.943680186733854,10.354692059415363,10.354216599850245,2.8598694107632285,1.8842301255437504,6.005765509106701,6.86264893854924,7.943680186733854,10.354692059415363,10.354216599850245,2.8598694107632285,1.8842301255437504,6.005765509106701,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,609.8,601.8,600.5,32.9,75.3,255.3,609.8,601.8,600.5,32.9,75.3,255.3,609.8,601.8,600.5,32.9,75.3,255.3,0,0,0,0 4 | O,1749.2,2014.7,1806.2,2890.1,1804.1,1140.5,3727.1,1749.2,2014.7,1806.2,2890.1,1804.1,1140.5,3727.1,1749.2,2014.7,1806.2,2890.1,1804.1,1140.5,3727.1,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_intermediate_files/PS_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.6377,0.0297 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.478,0.0293 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.4173,0.0292 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.2517,0.0016 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.0959,0.0124 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,1.0519,0.0851 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,1.0457,0.098 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.6605,0.0879 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,1.1698,0.1406 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,2.8805,0.0878 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,2.7563,0.0555 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,2.8307,0.1813 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_ORI/raw_data/PS_useful.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,yield_std,plaque_name,well_1 2 | 0.033,0.0068,50,0.026,10,2,0.15,0.1,3,0.15,0.02,0.4,50,0.075,4,10,0.6377,0.0297,PS,B2 3 | 0.165,0.0068,50,0.026,10,2,0.15,0.1,9,0.15,0.02,0.4,50,0.375,12,10,0.478,0.0293,PS,B3 4 | 0.099,0.0204,50,0.078,10,2,0.15,0.5,3,0.45,0.1,1.2,50,0.225,4,10,0.4173,0.0292,PS,B4 5 | 0.033,0.0204,50,0.078,10,2,0.15,0.5,9,0.45,0.06,2,50,0.225,12,10,0.2517,0.0016,PS,B5 6 | 0.33,0.068,0,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0,0.0037,PS,B6 7 | 0.33,0.068,50,0.26,10,2,1.5,1,30,1.5,0.2,4,50,0.75,40,10,0.0959,0.0124,PS,B7 8 | 0.165,0.034,50,0.026,10,2,0.75,0.5,15,0.45,0.02,2,50,0.225,20,10,1.0519,0.0851,PS,O2 9 | 0.099,0.034,50,0.026,10,2,0.75,0.3,15,0.75,0.02,1.2,50,0.375,20,10,1.0457,0.098,PS,O3 10 | 0.165,0.0204,50,0.078,10,2,0.75,0.5,9,0.15,0.02,0.4,50,0.375,20,10,0.6605,0.0879,PS,O4 11 | 0.033,0.0068,50,0.026,10,2,0.75,0.3,15,0.75,0.02,2,50,0.375,12,10,1.1698,0.1406,PS,O5 12 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,2.8805,0.0878,PS,O6 13 | 0.099,0.034,50,0.026,10,2,1.5,0.1,9,1.5,0.1,4,50,0.075,40,10,2.7563,0.0555,PS,O7 14 | 0.033,0.0204,50,0.078,10,2,1.5,0.1,9,1.5,0.06,4,50,0.075,40,10,2.8307,0.1813,PS,O8 15 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/analyse_regressions/regression_double_DNA_to_PS_PS_to_PS_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/analyse_regressions/regression_double_DNA_to_PS_PS_to_PS_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/analyse_regressions/regression_rifaxamin_to_PS_PS_to_PS_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/analyse_regressions/regression_rifaxamin_to_PS_PS_to_PS_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/analyse_regressions/regression_spectinomycin_PS_PS_to_PS_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/analyse_regressions/regression_spectinomycin_PS_PS_to_PS_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/duplicates/duplicated_double_DNA_to_PS_PS_to_PS_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/duplicates/duplicated_double_DNA_to_PS_PS_to_PS_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/duplicates/duplicated_rifaxamin_to_PS_PS_to_PS_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/duplicates/duplicated_rifaxamin_to_PS_PS_to_PS_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/duplicates/duplicated_spectinomycin_PS_PS_to_PS_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_plate_PS/duplicates/duplicated_spectinomycin_PS_PS_to_PS_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,5535.7,5676.7,3853.3,2932.3,1539.7,2166.3,5535.7,5676.7,3853.3,2932.3,1539.7,2166.3,5535.7,5676.7,3853.3,2932.3,1539.7,2166.3,0,0,0,0 3 | P,5994.0,8542.0,5296.3,8497.3,19150.3,17560.0,17293.3,5994.0,8542.0,5296.3,8497.3,19150.3,17560.0,17293.3,5994.0,8542.0,5296.3,8497.3,19150.3,17560.0,17293.3,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,1.5463265711653449,7.521975795796854,5.161809358212442,14.033352658322817,7.449503149964279,6.504177630060472,1.5463265711653449,7.521975795796854,5.161809358212442,14.033352658322817,7.449503149964279,6.504177630060472,1.5463265711653449,7.521975795796854,5.161809358212442,14.033352658322817,7.449503149964279,6.504177630060472,0,0,0,0 3 | P,17.76443109776443,10.777335518613908,6.685799520419916,6.723312110905817,4.3487569385336,5.065489749430524,9.674266912619338,17.76443109776443,10.777335518613908,6.685799520419916,6.723312110905817,4.3487569385336,5.065489749430524,9.674266912619338,17.76443109776443,10.777335518613908,6.685799520419916,6.723312110905817,4.3487569385336,5.065489749430524,9.674266912619338,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,85.6,427.0,198.9,411.5,114.7,140.9,85.6,427.0,198.9,411.5,114.7,140.9,85.6,427.0,198.9,411.5,114.7,140.9,0,0,0,0 3 | P,1064.8,920.6,354.1,571.3,832.8,889.5,1673.0,1064.8,920.6,354.1,571.3,832.8,889.5,1673.0,1064.8,920.6,354.1,571.3,832.8,889.5,1673.0,0 4 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/PS_intermediate_files/PS_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.5707,0.0122 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.5908,0.061 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.3304,0.0284 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.1989,0.0588 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.0895,0.0201 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,0.6361,0.1521 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,1.0,0.1315 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.5365,0.0506 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,0.9936,0.0816 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,2.515,0.1189 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,2.2879,0.127 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,2.2498,0.2389 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,17090.3,18855.0,7254.7,6257.3,1539.7,4165.0,17090.3,18855.0,7254.7,6257.3,1539.7,4165.0,17090.3,18855.0,7254.7,6257.3,1539.7,4165.0,0,0,0,0 4 | O,15392.3,24343.0,10712.0,22306.7,44145.7,43028.0,39104.3,15392.3,24343.0,10712.0,22306.7,44145.7,43028.0,39104.3,15392.3,24343.0,10712.0,22306.7,44145.7,43028.0,39104.3,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,2.8665383287595887,6.94510739856802,10.1727156188402,18.747702683265942,7.391050204585309,1.1164465786314526,2.8665383287595887,6.94510739856802,10.1727156188402,18.747702683265942,7.391050204585309,1.1164465786314526,2.8665383287595887,6.94510739856802,10.1727156188402,18.747702683265942,7.391050204585309,1.1164465786314526,0,0,0,0 4 | O,13.784814485164661,7.834695805775787,6.941747572815535,6.572464775157238,6.31046738413934,2.0588918843543738,4.688742670243426,13.784814485164661,7.834695805775787,6.941747572815535,6.572464775157238,6.31046738413934,2.0588918843543738,4.688742670243426,13.784814485164661,7.834695805775787,6.941747572815535,6.572464775157238,6.31046738413934,2.0588918843543738,4.688742670243426,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | B,489.9,1309.5,738.0,1173.1,113.8,46.5,489.9,1309.5,738.0,1173.1,113.8,46.5,489.9,1309.5,738.0,1173.1,113.8,46.5,0,0,0,0 4 | O,2121.8,1907.2,743.6,1466.1,2785.8,885.9,1833.5,2121.8,1907.2,743.6,1466.1,2785.8,885.9,1833.5,2121.8,1907.2,743.6,1466.1,2785.8,885.9,1833.5,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/double_DNA_intermediate_files/double_DNA_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,2.2208,0.07 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,2.4728,0.187 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.8162,0.1054 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.6737,0.1675 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.3749,0.0066 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,1.9783,0.303 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,3.2565,0.2724 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,1.3099,0.1062 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,2.9657,0.2094 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,6.0845,0.3978 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,5.9249,0.1265 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,5.3646,0.2618 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,1942.0,1667.0,1642.7,1586.3,1260.3,1486.0,1942.0,1667.0,1642.7,1586.3,1260.3,1486.0,1942.0,1667.0,1642.7,1586.3,1260.3,1486.0,0,0,0,0 4 | M,1869.7,1980.0,2174.7,2175.0,3028.3,2996.0,2596.0,1869.7,1980.0,2174.7,2175.0,3028.3,2996.0,2596.0,1869.7,1980.0,2174.7,2175.0,3028.3,2996.0,2596.0,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,12.883625128733264,0.9958008398320337,2.167163815669325,2.244216100359327,0.8807426803142109,2.5504710632570657,12.883625128733264,0.9958008398320337,2.167163815669325,2.244216100359327,0.8807426803142109,2.5504710632570657,12.883625128733264,0.9958008398320337,2.167163815669325,2.244216100359327,0.8807426803142109,2.5504710632570657,0,0,0,0 4 | M,3.8080975557576084,3.1868686868686873,2.5474778130316826,5.485057471264368,7.5917181256810755,6.268357810413885,3.054699537750385,3.8080975557576084,3.1868686868686873,2.5474778130316826,5.485057471264368,7.5917181256810755,6.268357810413885,3.054699537750385,3.8080975557576084,3.1868686868686873,2.5474778130316826,5.485057471264368,7.5917181256810755,6.268357810413885,3.054699537750385,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | D,250.2,16.6,35.6,35.6,11.1,37.9,250.2,16.6,35.6,35.6,11.1,37.9,250.2,16.6,35.6,35.6,11.1,37.9,0,0,0,0 4 | M,71.2,63.1,55.4,119.3,229.9,187.8,79.3,71.2,63.1,55.4,119.3,229.9,187.8,79.3,71.2,63.1,55.4,119.3,229.9,187.8,79.3,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/rifaxamin/rifaxamin_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.0936,0.0344 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.0558,0.0023 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.0525,0.0049 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.0448,0.0049 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.031,0.0052 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,0.0837,0.0098 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,0.0988,0.0087 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.1256,0.0076 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,0.1256,0.0164 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,0.2428,0.0316 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,0.2384,0.0258 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,0.1834,0.0109 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 13 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_draw_mean.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,3224.0,3005.3,2853.3,2492.3,1912.7,2221.0,3224.0,3005.3,2853.3,2492.3,1912.7,2221.0,3224.0,3005.3,2853.3,2492.3,1912.7,2221.0,0,0,0,0 4 | N,3049.3,2944.0,3389.7,3218.3,3325.0,3324.7,3502.0,3049.3,2944.0,3389.7,3218.3,3325.0,3324.7,3502.0,3049.3,2944.0,3389.7,3218.3,3325.0,3324.7,3502.0,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_draw_ratio.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,9.246277915632756,12.807373639902837,8.425332071636351,9.770091882999637,4.857008417420401,1.179648806843764,9.246277915632756,12.807373639902837,8.425332071636351,9.770091882999637,4.857008417420401,1.179648806843764,9.246277915632756,12.807373639902837,8.425332071636351,9.770091882999637,4.857008417420401,1.179648806843764,0,0,0,0 4 | N,3.387662742268717,2.5543478260869565,3.3011770953181703,2.7623279371096543,2.8781954887218046,3.9131350197010257,5.839520274129069,3.387662742268717,2.5543478260869565,3.3011770953181703,2.7623279371096543,2.8781954887218046,3.9131350197010257,5.839520274129069,3.387662742268717,2.5543478260869565,3.3011770953181703,2.7623279371096543,2.8781954887218046,3.9131350197010257,5.839520274129069,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_draw_std.csv: -------------------------------------------------------------------------------- 1 | row,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 2 | A,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 3 | C,298.1,384.9,240.4,243.5,92.9,26.2,298.1,384.9,240.4,243.5,92.9,26.2,298.1,384.9,240.4,243.5,92.9,26.2,0,0,0,0 4 | N,103.3,75.2,111.9,88.9,95.7,130.1,204.5,103.3,75.2,111.9,88.9,95.7,130.1,204.5,103.3,75.2,111.9,88.9,95.7,130.1,204.5,0 5 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_plate_PS/raw_data/spectomycin/spectinomycin_yield_and_std.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta,yield,yield_std 2 | 0.033,0.0068,0.026,0.15,0.1,3.0,0.15,0.02,0.4,0.075,4.0,0.1978,0.045 3 | 0.165,0.0068,0.026,0.15,0.1,9.0,0.15,0.02,0.4,0.375,12.0,0.1648,0.0581 4 | 0.099,0.0204,0.078,0.15,0.5,3.0,0.45,0.1,1.2,0.225,4.0,0.1419,0.0363 5 | 0.033,0.0204,0.078,0.15,0.5,9.0,0.45,0.06,2.0,0.225,12.0,0.0874,0.0367 6 | 0.33,0.068,0.26,1.5,1.0,30.0,1.5,0.2,4.0,0.75,40.0,0.0465,0.004 7 | 0.165,0.034,0.026,0.75,0.5,15.0,0.45,0.02,2.0,0.225,20.0,0.1715,0.0156 8 | 0.099,0.034,0.026,0.75,0.3,15.0,0.75,0.02,1.2,0.375,20.0,0.1556,0.0113 9 | 0.165,0.0204,0.078,0.75,0.5,9.0,0.15,0.02,0.4,0.375,20.0,0.2228,0.0169 10 | 0.033,0.0068,0.026,0.75,0.3,15.0,0.75,0.02,2.0,0.375,12.0,0.197,0.0134 11 | 0.165,0.068,0.026,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,0.213,0.0144 12 | 0.099,0.034,0.026,1.5,0.1,9.0,1.5,0.1,4.0,0.075,40.0,0.213,0.0196 13 | 0.033,0.0204,0.078,1.5,0.1,9.0,1.5,0.06,4.0,0.075,40.0,0.2397,0.0308 14 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_rifaxamin/analyse_regressions/regression_rifaxamin_rifaxamin_to_PS_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_rifaxamin/analyse_regressions/regression_rifaxamin_rifaxamin_to_PS_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_rifaxamin/duplicates/duplicated_rifaxamin_rifaxamin_to_PS_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_rifaxamin/duplicates/duplicated_rifaxamin_rifaxamin_to_PS_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_rifaxamin/raw_data/rifaxamin_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 115 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_rifaxamin/raw_data/rifaxamin_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /controls_analysis_plates/data_spectinomycin/analyse_regressions/regression_spectinomycin_spectinomycin_to_PS_yieldreg_ref.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_spectinomycin/analyse_regressions/regression_spectinomycin_spectinomycin_to_PS_yieldreg_ref.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_spectinomycin/duplicates/duplicated_spectinomycin_spectinomycin_to_PS_yield.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/controls_analysis_plates/data_spectinomycin/duplicates/duplicated_spectinomycin_spectinomycin_to_PS_yield.png -------------------------------------------------------------------------------- /controls_analysis_plates/data_spectinomycin/raw_data/spectinomycin_comments.txt: -------------------------------------------------------------------------------- 1 | There are 0 outliers out of 115 (0.0%) for CV of 30 -------------------------------------------------------------------------------- /controls_analysis_plates/data_spectinomycin/raw_data/spectinomycin_outliers.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,value_1,value_2,value_3,plaque_name 2 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/AB/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/AB/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/AB/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /multiple_extracts_analysis/DH5_alpha/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/DH5_alpha/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/DH5_alpha/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /multiple_extracts_analysis/ORI/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/ORI/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /multiple_extracts_analysis/ORI/showcase_1_model_vs_data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/ORI/showcase_1_model_vs_data.png -------------------------------------------------------------------------------- /multiple_extracts_analysis/PS/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/PS/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/PS/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /multiple_extracts_analysis/README.md: -------------------------------------------------------------------------------- 1 | # Description 2 | 3 | This folder contains data and scripts necessary to generate the most informative points for each new lysate, ie: the points that allow the best prediction of the rest of the dataset (Figure 2). 4 | 5 | 6 | # Data: 7 | 8 | Contains the whole data from this study. 9 | data/no_controls contains data from rows B to O, without controls from lines A and P. 10 | 11 | # 102_from_study: 12 | 13 | Contains the data for the 102 points that were used in this study for other plates. 14 | 15 | 16 | - ID_n_informative_points is the script that generated the points we used for the next steps (n varying between 8 and 24, Supplementary Figure 2e). Destination folder needs to exist. 17 | 18 | Randomly sampling combinations of experimental points, it chooses the best ones to predict the rest of the dataset. You need to ensure the destination folder for saving exists if you wish to use the script as it is. 19 | - verify_informative_points allows retraining of the selected combinations on the whole dataset; prediction functions are identical but wrapping allows for testing only the selected file. For 20 points, it can be used either with final_1.csv. 20 | 21 | Each folder with a lysate name contains resuls for this lysate. 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/final_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/rifaximin/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/rifaximin/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/rifaximin/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /multiple_extracts_analysis/spectinomycin/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /multiple_extracts_analysis/spectinomycin/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/multiple_extracts_analysis/spectinomycin/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /predict_for_new_lysate/AB/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /predict_for_new_lysate/AB/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/predict_for_new_lysate/AB/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /predict_for_new_lysate/AB_10000.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.33,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.5583,0.4014 3 | 0.33,0.068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.075,24.0,10,2.3236,0.5498 4 | 0.33,0.068,50,0.026,10,2,0.75,0.3,9.0,1.5,0.2,2.0,50,0.075,40.0,10,2.0484,0.7018 5 | 0.165,0.0068,50,0.26,10,2,0.15,0.1,9.0,1.5,0.02,4.0,50,0.075,80.0,10,2.0477,0.6788 6 | 0.165,0.068,50,0.13,10,2,0.15,0.1,9.0,1.5,0.2,2.0,50,0.075,8.0,10,1.8852,0.7933 7 | 0.33,0.034,50,0.26,10,2,0.75,0.1,9.0,1.5,0.2,2.0,50,0.075,40.0,10,1.9021,0.7548 8 | 0.165,0.034,50,0.26,10,2,0.45,0.1,9.0,1.5,0.2,4.0,50,0.075,80.0,10,2.1469,0.5808 9 | 0.33,0.068,50,0.26,10,2,0.15,0.1,9.0,1.5,0.06,4.0,50,0.075,40.0,10,1.8351,0.7782 10 | 0.33,0.068,50,0.026,10,2,0.75,0.5,9.0,1.5,0.2,4.0,50,0.225,40.0,10,1.9691,0.6815 11 | 0.033,0.0204,50,0.26,10,2,0.45,0.1,9.0,1.5,0.02,4.0,50,0.075,80.0,10,2.0208,0.6364 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/AB_10000_exploitation.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.33,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.5583,0.4014 3 | 0.165,0.034,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.4748,0.2909 4 | 0.099,0.034,50,0.078,10,2,1.5,0.1,9.0,1.5,0.1,4.0,50,0.075,80.0,10,2.453,0.1255 5 | 0.165,0.034,50,0.078,10,2,1.5,0.1,9.0,1.5,0.06,4.0,50,0.375,80.0,10,2.3809,0.1005 6 | 0.165,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.1,4.0,50,0.075,24.0,10,2.3459,0.1365 7 | 0.165,0.0204,50,0.026,10,2,0.75,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.3394,0.2301 8 | 0.033,0.068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.1,4.0,50,0.075,80.0,10,2.3258,0.1491 9 | 0.33,0.068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.075,24.0,10,2.3236,0.5498 10 | 0.33,0.0068,50,0.13,10,2,1.5,0.1,9.0,1.5,0.1,4.0,50,0.075,40.0,10,2.3154,0.1911 11 | 0.033,0.034,50,0.026,10,2,0.75,0.1,9.0,1.5,0.1,4.0,50,0.225,80.0,10,2.3094,0.271 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/AB_10000_exploration.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.33,0.068,50,0.26,10,2,0.15,0.1,9.0,1.5,0.1,0.4,50,0.075,8.0,10,1.445,0.8995 3 | 0.33,0.068,50,0.26,10,2,0.45,0.1,9.0,1.5,0.06,0.4,50,0.075,24.0,10,1.4576,0.8067 4 | 0.165,0.068,50,0.13,10,2,0.15,0.1,9.0,1.5,0.2,0.4,50,0.075,24.0,10,1.7745,0.7973 5 | 0.165,0.068,50,0.13,10,2,0.15,0.1,9.0,1.5,0.2,2.0,50,0.075,8.0,10,1.8852,0.7933 6 | 0.33,0.034,50,0.26,10,2,0.15,0.5,9.0,1.5,0.2,4.0,50,0.225,8.0,10,1.5859,0.793 7 | 0.33,0.068,50,0.13,10,2,0.15,0.3,9.0,1.5,0.2,0.4,50,0.225,24.0,10,1.6058,0.7855 8 | 0.33,0.068,50,0.26,10,2,0.15,0.1,9.0,1.5,0.06,4.0,50,0.075,40.0,10,1.8351,0.7782 9 | 0.33,0.068,50,0.13,10,2,0.45,0.1,9.0,0.75,0.2,4.0,50,0.075,24.0,10,1.7559,0.7695 10 | 0.165,0.0204,50,0.26,10,2,0.15,0.1,9.0,1.5,0.2,0.4,50,0.075,8.0,10,1.5699,0.768 11 | 0.33,0.034,50,0.26,10,2,0.45,0.5,9.0,1.5,0.2,1.2,50,0.075,8.0,10,1.4605,0.7565 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/ORI/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/predict_for_new_lysate/ORI/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /predict_for_new_lysate/ORI/showcase_1_model_vs_data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/predict_for_new_lysate/ORI/showcase_1_model_vs_data.png -------------------------------------------------------------------------------- /predict_for_new_lysate/ORI_10000.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.033,0.0068,50,0.13,10,2,1.5,0.1,9.0,1.5,0.06,4.0,50,0.375,80.0,10,2.2158,0.2977 3 | 0.099,0.0068,50,0.26,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.075,80.0,10,2.299,0.2315 4 | 0.099,0.0068,50,0.078,10,2,0.75,0.1,9.0,1.5,0.2,4.0,50,0.075,80.0,10,2.4298,0.1328 5 | 0.033,0.0068,50,0.26,10,2,0.75,0.3,9.0,1.5,0.2,4.0,50,0.075,80.0,10,2.0686,0.3739 6 | 0.033,0.0068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.5255,0.0443 7 | 0.033,0.0068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.75,80.0,10,1.9917,0.4159 8 | 0.099,0.0068,50,0.026,10,2,0.75,0.1,9.0,1.5,0.2,4.0,50,0.375,80.0,10,2.1785,0.2694 9 | 0.165,0.0068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,2.0,50,0.075,80.0,10,2.3614,0.1226 10 | 0.033,0.034,50,0.13,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.3123,0.1507 11 | 0.033,0.034,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.375,80.0,10,2.2234,0.2075 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/ORI_10000_exploitation.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.033,0.0068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.5255,0.0443 3 | 0.099,0.0068,50,0.078,10,2,0.75,0.1,9.0,1.5,0.2,4.0,50,0.075,80.0,10,2.4298,0.1328 4 | 0.165,0.0068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,2.0,50,0.075,80.0,10,2.3614,0.1226 5 | 0.033,0.034,50,0.13,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.3123,0.1507 6 | 0.099,0.0068,50,0.26,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.075,80.0,10,2.299,0.2315 7 | 0.165,0.0068,50,0.13,10,2,1.5,0.1,9.0,1.5,0.2,2.0,50,0.075,80.0,10,2.2879,0.0887 8 | 0.165,0.0204,50,0.026,10,2,0.75,0.1,9.0,1.5,0.1,4.0,50,0.075,80.0,10,2.2699,0.0827 9 | 0.165,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.06,4.0,50,0.225,80.0,10,2.2551,0.1005 10 | 0.099,0.0068,50,0.13,10,2,1.5,0.1,9.0,1.5,0.06,2.0,50,0.075,80.0,10,2.2394,0.1069 11 | 0.033,0.034,50,0.078,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.375,80.0,10,2.2234,0.2075 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/ORI_10000_exploration.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.33,0.068,50,0.26,10,2,0.15,1.0,9.0,0.75,0.02,2.0,50,0.75,24.0,10,-0.7581,1.0969 3 | 0.33,0.068,50,0.26,10,2,0.45,1.0,9.0,1.5,0.02,4.0,50,0.75,80.0,10,-0.2789,1.0708 4 | 0.099,0.068,50,0.26,10,2,0.75,1.0,9.0,1.5,0.02,4.0,50,0.75,80.0,10,0.1005,1.064 5 | 0.165,0.034,50,0.078,10,2,0.15,1.0,9.0,1.5,0.02,4.0,50,0.75,80.0,10,0.4568,1.0596 6 | 0.33,0.068,50,0.26,10,2,0.15,1.0,9.0,0.75,0.06,2.0,50,0.75,24.0,10,-0.7589,1.0525 7 | 0.33,0.0204,50,0.26,10,2,0.45,1.0,9.0,0.45,0.02,4.0,50,0.75,80.0,10,-0.0458,1.0507 8 | 0.33,0.034,50,0.26,10,2,0.15,1.0,9.0,0.15,0.02,0.4,50,0.75,8.0,10,-0.6809,1.0498 9 | 0.33,0.068,50,0.26,10,2,0.45,1.0,9.0,0.15,0.02,0.4,50,0.75,24.0,10,-0.7826,1.047 10 | 0.099,0.068,50,0.26,10,2,0.75,1.0,9.0,1.5,0.02,4.0,50,0.75,40.0,10,-0.2391,1.0337 11 | 0.165,0.0068,50,0.26,10,2,0.15,1.0,9.0,1.5,0.02,2.0,50,0.75,80.0,10,0.0884,1.031 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/PS/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /predict_for_new_lysate/PS/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/predict_for_new_lysate/PS/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /predict_for_new_lysate/PS_10000.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9.0,0.75,0.02,4.0,50,0.075,80.0,10,1.9325,0.1853 3 | 0.165,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.06,4.0,50,0.225,80.0,10,2.0732,0.0706 4 | 0.099,0.0068,50,0.078,10,2,0.75,0.1,9.0,1.5,0.02,4.0,50,0.225,40.0,10,1.7131,0.321 5 | 0.099,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.0775,0.0541 6 | 0.033,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.1006,0.0337 7 | 0.165,0.0068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.225,24.0,10,1.8132,0.2358 8 | 0.033,0.0068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.1051,0.0261 9 | 0.165,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.375,40.0,10,1.8701,0.192 10 | 0.165,0.0068,50,0.078,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.075,8.0,10,1.7577,0.2548 11 | 0.033,0.0068,50,0.26,10,2,1.5,0.1,9.0,0.75,0.02,4.0,50,0.375,80.0,10,1.6492,0.3183 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/PS_10000_exploitation.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.033,0.0068,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.1051,0.0261 3 | 0.033,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.1006,0.0337 4 | 0.099,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.2,4.0,50,0.225,80.0,10,2.0775,0.0541 5 | 0.165,0.034,50,0.026,10,2,1.5,0.1,9.0,1.5,0.06,4.0,50,0.225,80.0,10,2.0732,0.0706 6 | 0.165,0.068,50,0.026,10,2,1.5,0.1,9.0,0.75,0.02,4.0,50,0.075,80.0,10,1.9325,0.1853 7 | 0.33,0.0204,50,0.026,10,2,1.5,0.1,9.0,0.75,0.02,4.0,50,0.075,80.0,10,1.9038,0.1193 8 | 0.033,0.068,50,0.078,10,2,1.5,0.3,9.0,1.5,0.02,4.0,50,0.225,80.0,10,1.8926,0.0266 9 | 0.165,0.0204,50,0.026,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.375,40.0,10,1.8701,0.192 10 | 0.165,0.0204,50,0.078,10,2,1.5,0.1,9.0,1.5,0.02,4.0,50,0.225,40.0,10,1.8617,0.1669 11 | 0.033,0.068,50,0.026,10,2,0.75,0.1,9.0,1.5,0.1,4.0,50,0.225,80.0,10,1.8563,0.0995 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/PS_10000_exploration.csv: -------------------------------------------------------------------------------- 1 | nad,folinic_acid,DNA,coa,RBS,peg,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,hepes,camp,K_gluta,promoter,yield,std 2 | 0.033,0.0068,50,0.26,10,2,0.75,1.0,9.0,0.45,0.2,4.0,50,0.375,8.0,10,0.1876,0.6968 3 | 0.033,0.0068,50,0.13,10,2,1.5,1.0,9.0,0.45,0.1,0.4,50,0.75,8.0,10,0.0481,0.6832 4 | 0.033,0.0068,50,0.078,10,2,1.5,1.0,9.0,0.45,0.2,2.0,50,0.75,8.0,10,0.0823,0.683 5 | 0.033,0.0068,50,0.13,10,2,0.45,1.0,9.0,0.15,0.2,4.0,50,0.75,8.0,10,0.1278,0.6421 6 | 0.033,0.0068,50,0.078,10,2,0.75,1.0,9.0,1.5,0.1,4.0,50,0.75,8.0,10,0.4541,0.6311 7 | 0.033,0.0068,50,0.13,10,2,1.5,1.0,9.0,0.15,0.02,0.4,50,0.75,8.0,10,0.0733,0.6273 8 | 0.033,0.0068,50,0.13,10,2,0.45,1.0,9.0,0.75,0.2,4.0,50,0.75,8.0,10,0.1867,0.6239 9 | 0.033,0.0068,50,0.13,10,2,1.5,1.0,9.0,0.15,0.2,4.0,50,0.075,8.0,10,0.1111,0.6196 10 | 0.099,0.0204,50,0.13,10,2,1.5,1.0,9.0,0.75,0.02,4.0,50,0.75,8.0,10,0.5499,0.6117 11 | 0.033,0.0204,50,0.13,10,2,1.5,1.0,9.0,0.15,0.2,1.2,50,0.375,8.0,10,0.0317,0.6043 12 | -------------------------------------------------------------------------------- /predict_for_new_lysate/README.md: -------------------------------------------------------------------------------- 1 | # 21/08/19: 2 | 3 | Aim: Provide a script that given the results from the 20 combinations suggested returns the best combination to try. 4 | 5 | Takes as input a csv file with the values from the experiments of interest for which to predict best combinations to test. 6 | -------------------------------------------------------------------------------- /whole_lysate_most_informative_points/102_from_study/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brsynth/active_learning_cell_free/52816965250802a9243183ee391da7c09f08f069/whole_lysate_most_informative_points/102_from_study/showcase_1_model_vs_data.jpeg -------------------------------------------------------------------------------- /whole_lysate_most_informative_points/102_most_informative/final_1_model_vs_data.png: 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nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /whole_lysate_most_informative_points/20_most_informative/showcase_1.csv: -------------------------------------------------------------------------------- 1 | # nad,folinic_acid,coa,nucleo_mix,spermidin,pga,aa,trna,mg_gluta,camp,K_gluta 2 | 0.033,0.0204,0.026,0.75,0.3,3,0.15,0.02,1.2,0.075,8 3 | 0.165,0.0068,0.078,1.5,0.1,9,0.45,0.02,4,0.075,80 4 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.02,4,0.225,80 5 | 0.165,0.034,0.078,1.5,0.1,9,1.5,0.1,4,0.375,80 6 | 0.099,0.0204,0.026,1.5,0.1,9,1.5,0.06,4,0.075,80 7 | 0.099,0.0068,0.026,1.5,0.3,9,0.15,0.2,4,0.075,80 8 | 0.165,0.034,0.026,1.5,0.1,9,1.5,0.1,4,0.075,80 9 | 0.33,0.068,0.26,1.5,0.1,30,1.5,0.2,4,0.75,80 10 | 0.033,0.034,0.078,0.75,0.1,9,0.45,0.1,2,0.075,40 11 | 0.033,0.0204,0.026,1.5,0.1,9,1.5,0.1,2,0.075,80 12 | 0.033,0.0068,0.078,1.5,0.1,9,0.75,0.2,4,0.075,80 13 | 0.033,0.0068,0.078,1.5,1,9,0.45,0.06,4,0.075,80 14 | 0.033,0.0068,0.026,0.45,0.3,15,0.15,0.1,2,0.225,40 15 | 0.099,0.034,0.13,0.75,0.3,15,0.15,0.06,1.2,0.075,40 16 | 0.033,0.0068,0.026,1.5,1,9,0.45,0.1,4,0.075,80 17 | 0.033,0.034,0.026,0.75,0.3,15,0.45,0.1,2,0.225,40 18 | 0.165,0.0204,0.078,0.45,0.3,9,0.45,0.1,0.4,0.225,24 19 | 0.033,0.034,0.13,1.5,0.3,9,0.15,0.02,4,0.075,80 20 | 0.033,0.0068,0.078,1.5,0.1,9,1.5,0.2,4,0.375,80 21 | 0.099,0.034,0.026,0.75,0.3,15,0.45,0.02,2,0.225,40 22 | -------------------------------------------------------------------------------- /whole_lysate_most_informative_points/20_most_informative/showcase_1_model_vs_data.jpeg: -------------------------------------------------------------------------------- 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