MANIFEST.in
README.md
pyproject.toml
requirements.txt
requirements_pyvista.txt
setup.py
crisscross/README.md
crisscross/__init__.py
crisscross/cli_functions/__init__.py
crisscross/cli_functions/handle_evolution.py
crisscross/cli_functions/plate_resuspension.py
crisscross/cli_functions/working_stock_creation.py
crisscross/core_functions/__init__.py
crisscross/core_functions/megastructure_composition.py
crisscross/core_functions/megastructures.py
crisscross/core_functions/plate_handling.py
crisscross/core_functions/slat_design.py
crisscross/core_functions/slats.py
crisscross/core_functions/stepwise_plots.py
crisscross/dna_source_plates/assembly_plates/P3250_SW_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3251_CW_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3252_SW_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3533_SW_handles.xlsx
crisscross/dna_source_plates/assembly_plates/P3534_SW_handles.xlsx
crisscross/dna_source_plates/assembly_plates/P3535_SW_handles.xlsx
crisscross/dna_source_plates/assembly_plates/P3536_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3537_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3538_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/assembly_plates/P3601_MA_H5_handles_S1A.xlsx
crisscross/dna_source_plates/assembly_plates/P3602_MA_H5_handles_S1B.xlsx
crisscross/dna_source_plates/assembly_plates/P3603_MA_H5_handles_S1C.xlsx
crisscross/dna_source_plates/assembly_plates/P3604_MA_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/assembly_plates/P3605_MA_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/assembly_plates/P3606_MA_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/assembly_plates/P3649_MA_H5_handles_S1A.xlsx
crisscross/dna_source_plates/assembly_plates/P3650_MA_H5_handles_S1B.xlsx
crisscross/dna_source_plates/assembly_plates/P3651_MA_H5_handles_S1C.xlsx
crisscross/dna_source_plates/assembly_plates/P3652_MA_H5_handles_S2A.xlsx
crisscross/dna_source_plates/assembly_plates/P3653_MA_H5_handles_S2B.xlsx
crisscross/dna_source_plates/assembly_plates/P3654_MA_H5_handles_S2C.xlsx
crisscross/dna_source_plates/assembly_plates/P3655_MA_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/assembly_plates/P3656_MA_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/assembly_plates/P3657_MA_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/assembly_plates/P3658_MA_H2_antihandles_S2A.xlsx
crisscross/dna_source_plates/assembly_plates/P3659_MA_H2_antihandles_S2B.xlsx
crisscross/dna_source_plates/assembly_plates/P3660_MA_H2_antihandles_S2C.xlsx
crisscross/dna_source_plates/cargo_plates/P3510_SSW_cnt_patterning.xlsx
crisscross/dna_source_plates/cargo_plates/P3518_MA_octahedron_patterning_v1.xlsx
crisscross/dna_source_plates/cargo_plates/P3628_SSW_plate.xlsx
crisscross/dna_source_plates/cargo_plates/sw_src004_polyAgridiron.xlsx
crisscross/dna_source_plates/cargo_plates/sw_src005_antiNelsonQuimby_cc6hb_h2handles.xlsx
crisscross/dna_source_plates/cargo_plates/sw_src007_nelson_quimby_bart_edna.xlsx
crisscross/dna_source_plates/cargo_plates/sw_src010_nelson_quimby_bart_edna_maxed.xlsx
crisscross/dna_source_plates/flat_staple_plates/sw_src002_slatcore.xlsx
crisscross/dna_source_plates/flat_staple_plates/sw_src009_control_max.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3250_SW_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3251_CW_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3252_SW_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3533_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3534_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3535_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3536_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3537_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3538_MA_h2_antihandles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3601_MA_H5_handles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3602_MA_H5_handles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3603_MA_H5_handles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3604_MA_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3605_MA_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3606_MA_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3649_MA_H5_handles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3650_MA_H5_handles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3651_MA_H5_handles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3652_MA_H5_handles_S2A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3653_MA_H5_handles_S2B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3654_MA_H5_handles_S2C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3655_MA_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3656_MA_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3657_MA_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3658_MA_H2_antihandles_S2A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3659_MA_H2_antihandles_S2B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/P3660_MA_H2_antihandles_S2C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3649_MA_H5_handles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3650_MA_H5_handles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3651_MA_H5_handles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3652_MA_H5_handles_S2A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3653_MA_H5_handles_S2B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3654_MA_H5_handles_S2C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3655_MA_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3656_MA_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3657_MA_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3658_MA_H2_antihandles_S2A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3659_MA_H2_antihandles_S2B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_order_sheets/IDT_ORDER_P3660_MA_H2_antihandles_S2C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_spec_sheets/batch_1.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_spec_sheets/batch_2.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_spec_sheets/batch_3.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/maximal_order/IDT_spec_sheets/batch_4.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3601_FK_H5_handles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3602_FK_H5_handles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3603_FK_H5_handles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3604_FK_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3605_FK_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets/IDT_ORDER_P3606_FK_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3601_FK_H5_handles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3602_FK_H5_handles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3603_FK_H5_handles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3604_FK_H2_antihandles_S1A.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3605_FK_H2_antihandles_S1B.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_order_sheets_obfuscated/IDT_ORDER_SCRAMBLED_P3606_FK_H2_antihandles_S1C.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_plate_specs/3601-3603.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/new_assembly_handle_library_orders/order_1_test/IDT_plate_specs/3604-3606.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/not ordered/PX1_MA_h2_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/not ordered/PX2_MA_h2_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/not ordered/PX3_MA_h2_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/previous_names/P3247_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/previous_names/P3248_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/assembly_handle_plates/previous_names/P3249_SW_handles.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/P3510_SSW_biotin_obsolete.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/P3510_SSW_cnt_patterning.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/P3518_MA_octahedron_patterning_v1.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/P3628_SSW_plate.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/sw_src004_polyAgridiron.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/sw_src005_antiNelsonQuimby_cc6hb_h2handles.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/sw_src007_nelson_quimby_bart_edna.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/sw_src008_lef1-scramble-7hb.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/sw_src010_nelson_quimby_bart_edna_maxed.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/old_format/P3518_MA_octahedron_patterning_v1.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/old_format/sw_src005_antiNelsonQuimby_cc6hb_h2handles.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/old_format/sw_src007_nelson_quimby_bart_edna.xlsx
crisscross/dna_source_plates/old_plate_format/cargo_plates/spec_sheets/P3628_specs.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P2854_CW_seed_plug_center.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P3339_JL_seed_plug_corner.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P3555_SSW_combined_seeds.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P3578_SSW_3primeTT.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P3621_SSW_seed_plug_center_8064.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/P3643_MA_combined_seeds_8064.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/sw_src001_seedcore.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/sw_src002_slatcore.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/sw_src004_polyAgridiron.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/sw_src009_control_max.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/spec_sheets/P3621_specs.xlsx
crisscross/dna_source_plates/old_plate_format/core_plates/spec_sheets/P3643_specs.xlsx
crisscross/dna_source_plates/seed_plates/P2854_CW_seed_plug_center.xlsx
crisscross/dna_source_plates/seed_plates/P3339_JL_seed_plug_corner.xlsx
crisscross/dna_source_plates/seed_plates/P3555_SSW_combined_seeds.xlsx
crisscross/dna_source_plates/seed_plates/P3621_SSW_seed_plug_center_8064.xlsx
crisscross/dna_source_plates/seed_plates/P3643_MA_combined_seeds_8064.xlsx
crisscross/graphics/__init__.py
crisscross/graphics/blender_3d.py
crisscross/graphics/pyvista_3d.py
crisscross/graphics/static_plots.py
crisscross/helper_functions/__init__.py
crisscross/helper_functions/lab_helper_sheet_generation.py
crisscross/helper_functions/simple_plate_visuals.py
crisscross/helper_functions/slat_salient_quantities.py
crisscross/helper_functions/slurm_process_and_run.py
crisscross/helper_functions/standard_sequences.py
crisscross/plate_mapping/__init__.py
crisscross/plate_mapping/hash_cad_plates.py
crisscross/plate_mapping/plate_constants.py
crisscross/plate_mapping/non_standard_plates/__init__.py
crisscross/plate_mapping/non_standard_plates/cargo_plates.py
crisscross/plate_mapping/non_standard_plates/core_plates.py
crisscross/plate_mapping/non_standard_plates/crisscross_plates.py
crisscross/plate_mapping/non_standard_plates/hash_cad_plate_converter.py
crisscross/plate_mapping/non_standard_plates/hybrid_plates.py
crisscross/plate_mapping/non_standard_plates/old_cargo_plates.py
crisscross/plate_mapping/non_standard_plates/plate_concentrations.py
crisscross/plate_mapping/non_standard_plates/seed_plates.py
crisscross/scripts/handle_evolution/64_seq_square_test.py
crisscross/scripts/handle_evolution/batch_file_generation_round_1.py
crisscross/scripts/handle_evolution/debugging_evolution.py
crisscross/scripts/handle_evolution/debugging_multi_split_evolution.py
crisscross/scripts/handle_evolution/heatmap_experiment_analysis.py
crisscross/scripts/handle_evolution/hyperparam_sweep_1.py
crisscross/scripts/handle_evolution/library_sweep_optuna_optimized.py
crisscross/scripts/handle_evolution/multi_run_quick_comparison.py
crisscross/scripts/handle_evolution/optimization_with_optuna.py
crisscross/scripts/handle_evolution/optuna_sweep_quick_graph.py
crisscross/scripts/handle_evolution/optuna_viz.py
crisscross/scripts/handle_evolution/unfinished_scripts/hyperparam_sweep_2.py
crisscross/scripts/handle_evolution/unfinished_scripts/results_interp_2d.py
crisscross/scripts/handle_evolution/unfinished_scripts/results_interpretation.py
crisscross/scripts/katzi/analyse_echo_plate_usage/analyse_echo_survey.py
crisscross/scripts/katzi/analyse_echo_plate_usage/analyse_echo_survey_2.py
crisscross/scripts/katzi/analyse_echo_plate_usage/awergtrea.py
crisscross/scripts/katzi/analyse_echo_plate_usage/test.py
crisscross/scripts/katzi/evolution_analysis/analyse_evo.py
crisscross/scripts/katzi/evolution_analysis/file_renamer.py
crisscross/scripts/katzi/evolution_analysis/plot_distributions.py
crisscross/scripts/katzi/evolution_analysis/plot_things.py
crisscross/scripts/katzi/evolution_analysis/plot_things2.py
crisscross/scripts/katzi/evolution_analysis/run_evo.py
crisscross/scripts/katzi/test_C_code_eqcorr2d/verify_results_eqcorr2d.py
crisscross/scripts/megastructure_designs/3d_folding_cube/CB015_echo_prep.py
crisscross/scripts/megastructure_designs/3d_folding_cube/CB015_handle_evolution.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/CAPC_v1.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/CAPC_v2_hexagon.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/capc_pattern_generator.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/handle_evolution.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/preliminary_work/CAPC_v1.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/preliminary_work/H5_bart_edna_handle_library_generation.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/preliminary_work/K99_designs_v2.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/preliminary_work/creating_designs_for_fellowships.py
crisscross/scripts/megastructure_designs/antigen_presenting_cells/preliminary_work/design_display.py
crisscross/scripts/megastructure_designs/bionwire_collab/design_v1_visualization.py
crisscross/scripts/megastructure_designs/bionwire_collab/design_v2_wider_trench.py
crisscross/scripts/megastructure_designs/bionwire_collab/unfinished_designs/crossbar_example.py
crisscross/scripts/megastructure_designs/bionwire_collab/unfinished_designs/deep_trench.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_1_2024/3D_stairs_handle_evolution.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_1_2024/7_layer_viz.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_1_2024/design_setup_and_visualisation.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_2_march_2025/design_setup_and_echo_export.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_2_march_2025/echo_combining_script.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_2_march_2025/evolution_version_2.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/3D_stacking/version_3_april_2025/evolution.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/TMSD/basic_designs.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/TMSD/basic_designs_v2_incomplete.py
crisscross/scripts/megastructure_designs/early_megastructure_designs/TMSD/basic_designs_v3_no_knock_in.py
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