parresgold_2023_dimer_networks_code.zip
parresgold_2023_dimer_networks_code
analyze_1D_screen.ipynb
3.0 MB
analyze_2D_screen.ipynb
269.7 kB
analyze_connectivity_trends.ipynb
1.9 MB
analyze_equilibration_kinetics.ipynb
665.5 kB
analyze_expression_noise_robustness.ipynb
674.0 kB
analyze_intrinsic_noise.ipynb
593.7 kB
boolean_complexity.ipynb
100.3 kB
dimer_network_utilities.py
35.4 kB
generate_param_screen.ipynb
35.0 kB
optimizer_dualannealing.ipynb
335.6 kB
randomK_versatility_optimization_trials
code
makefuncs.py
5.5 kB
opt_utils.py
21.6 kB
summarize_plots.py
2.6 kB
tuning.py
55.9 kB
utilities.py
11.4 kB
data
2d
custom_2D_target_names.npy
788 Bytes
custom_2D_targets.npy
12.8 kB
K_sets
8M_connectivity.npy
19.1 kB
voxel_averages
10M_voxel_averages.npy
161.9 kB
11M_voxel_averages.npy
166.0 kB
12M_voxel_averages.npy
165.0 kB
2M_voxel_averages.npy
40.0 kB
3M_voxel_averages.npy
92.5 kB
4M_voxel_averages.npy
112.0 kB
5M_voxel_averages.npy
129.0 kB
6M_voxel_averages.npy
137.9 kB
7M_voxel_averages.npy
146.0 kB
8M_voxel_averages.npy
151.8 kB
9M_voxel_averages.npy
156.6 kB
requirements.txt
3.9 kB
requirements2.txt
3.4 kB
run_scripts
bump_inference_tests_ainner_BoundedBumpsSeparate_main.py
3.7 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK.py
3.8 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK_jacobTargets.py
4.1 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK_jacobTargets_perDimer.py
5.9 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK_jacobTargets_perDimer_multi.py
6.9 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK_jacobTargets_perDimer_ray.py
11.8 kB
bump_inference_tests_ainner_BoundedBumpsSeparate_main_randomK_jacobTargets_perDimer_ray_2D.py
14.5 kB
full_run1.sh
368 Bytes
full_run2.sh
463 Bytes
full_run2_2d.sh
366 Bytes
full_run2_specialKs_m8.sh
406 Bytes
inference_tests_1.py
7.4 kB
inference_tests_3m_univ485.py
7.4 kB
inference_tests_3m_univ485_cluster.py
6.8 kB
inner_opt_tests.py
3.8 kB
job_trier.py
36.1 kB
job_trier2.py
7.6 kB
metacluster_inference_tests_1.py
4.6 kB
metacluster_inference_tests_1_ainner.py
4.7 kB
opt_script_pymoo.py
3.8 kB
pilot_run1.sh
313 Bytes
randomK_scriptGen.py
1.8 kB
randomK_scriptGen2.py
1.7 kB
setup_AWS.sh
1.1 kB
summarize_targets.py
1.2 kB
remake_Fig1.ipynb
181.4 kB
remake_Fig2.ipynb
142.1 kB
remake_Fig3.ipynb
687.8 kB
remake_Fig4.ipynb
5.0 MB
remake_Fig5.ipynb
615.7 kB
remake_Fig6.ipynb
1.9 MB
remake_FigS5.ipynb
2.5 MB
remake_FigS7.ipynb
186.1 kB
remake_GraphicalAbstract.ipynb
62.1 kB
separation_of_timescales.ipynb
626.8 kB
simulate_individual_networks.ipynb
172.9 kB
versatility_expression_changes.ipynb
272.3 kB