├── .gitattributes ├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── README.md ├── assets └── aggregated_data │ ├── mouse_me_and_met_avg_layer_depths.json │ └── rnaseq_sorted_cre.pkl ├── ateamopt ├── __init__.py ├── analysis │ ├── __init__.py │ ├── allactive_classification.py │ ├── analysis_module.py │ ├── optim_analysis.py │ └── sensitivity_analysis.py ├── animation │ ├── __init__.py │ └── animation_module.py ├── bpopt_evaluator.py ├── cell_data.py ├── jobscript │ ├── __init__.py │ ├── jobmodule.py │ ├── launch_optimjob.py │ └── submit_opt_jobs ├── model_parameters.py ├── morph_handler.py ├── nwb_extractor.py ├── optim_config_rules.py ├── optim_schema.py ├── scripts │ ├── Optim_Main.py │ ├── __init__.py │ ├── analyze_stagejob.py │ ├── iopubwatcher.py │ └── prepare_stagejob.py ├── template │ ├── __init__.py │ ├── data_transfer │ │ ├── aibs_local_transfer.sh │ │ ├── aws_datapath.sh │ │ ├── aws_transfer_to_local.sh │ │ ├── bbp_datapath.sh │ │ ├── bbp_transfer_to_local.sh │ │ ├── nersc_datapath.sh │ │ ├── nersc_transfer_to_local.sh │ │ └── wasabi_transfer_to_local.sh │ ├── job_templates │ │ ├── bbp_slurm_jobtemplate.sh │ │ ├── chainjob_template.sh │ │ ├── nersc_slurm_jobtemplate.sh │ │ ├── pbs_jobtemplate.sh │ │ └── sge_jobtemplate.sh │ └── parameters │ │ ├── param_bounds_human_exc.json │ │ ├── param_bounds_humn_inh.json │ │ ├── param_bounds_mouse_exc.json │ │ └── param_bounds_mouse_inh.json ├── tests │ ├── __init__.py │ ├── test_data │ │ ├── __init__.py │ │ ├── mouse_aspiny │ │ │ └── __init__.py │ │ └── mouse_spiny │ │ │ ├── Stage0_features.json │ │ │ ├── Stage0_mechanism.json │ │ │ ├── Stage0_parameters.json │ │ │ ├── Stage0_protocols.json │ │ │ └── __init__.py │ └── test_init.py └── utils │ ├── __init__.py │ └── utility.py ├── aws └── README.md ├── docker ├── Dockerfile └── requirements.txt ├── examples ├── ipyparallel │ ├── avg_fi_parallel.py │ └── fi_parallel_pbs.sh ├── optim_scripts │ ├── feature_set_all.json │ ├── feature_set_stage0.json │ ├── feature_set_stage1.json │ ├── feature_set_stage2.json │ ├── job_config.json │ ├── modfiles │ │ ├── BK_gc.mod │ │ ├── CaDynamics.mod │ │ ├── Ca_HVA.mod │ │ ├── Ca_LVA.mod │ │ ├── Cabuffer_gc.mod │ │ ├── Cav12_gc.mod │ │ ├── Cav13_gc.mod │ │ ├── Cav22_gc.mod │ │ ├── Cav32_gc.mod │ │ ├── HCN_gc.mod │ │ ├── Ih.mod │ │ ├── Im.mod │ │ ├── Im_v2.mod │ │ ├── K_P.mod │ │ ├── K_Pst.mod │ │ ├── K_T.mod │ │ ├── K_Tst.mod │ │ ├── Kd.mod │ │ ├── Kir21_gc.mod │ │ ├── Kv11_gc.mod │ │ ├── Kv14_gc.mod │ │ ├── Kv21_gc.mod │ │ ├── Kv2like.mod │ │ ├── Kv34_gc.mod │ │ ├── Kv3_1.mod │ │ ├── Kv42_gc.mod │ │ ├── Kv723_gc.mod │ │ ├── NaTa.mod │ │ ├── NaTa_t.mod │ │ ├── NaTg.mod │ │ ├── NaTs.mod │ │ ├── NaTs2_t.mod │ │ ├── NaV.mod │ │ ├── Nap.mod │ │ ├── Nap_Et2.mod │ │ ├── SK.mod │ │ ├── SK2_gc.mod │ │ └── na8st_gc.mod │ ├── param_bounds_stage0.json │ ├── param_bounds_stage1.json │ └── param_bounds_stage2.json ├── sensititvity_analysis │ ├── sa_example.py │ └── sens_analysis_pbs.sh └── visualization │ ├── 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