.dockerignore
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.env.run-local
.env.test-docker
.env.test-local
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CONTRIBUTIONS.md
Dockerfile
LICENSE
Makefile
README.md
docker-cmd.sh
docker-compose.run.yml
docker-compose.test.yml
docker-compose.yml
pyproject.toml
uv.lock
.github/workflows/publish-pypi.yml
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app/__init__.py
app/__main__.py
app/application.py
app/config.py
app/errors.py
app/logger.py
app/dependencies/__init__.py
app/dependencies/auth.py
app/dependencies/entitysdk.py
app/endpoints/__init__.py
app/endpoints/declared_endpoints.py
app/endpoints/generated_endpoints.py
app/endpoints/licenses.py
app/endpoints/mtypes.py
app/endpoints/subject_data.py
app/schemas/__init__.py
app/schemas/auth.py
app/schemas/base.py
app/utils/__init__.py
app/utils/common.py
app/utils/http.py
examples/A_service_and_entitycore/circuit_simulation/entitysdk_circuit_simulations.ipynb
examples/A_service_and_entitycore/deserialize/deserialize_example.ipynb
examples/A_service_and_entitycore/multiservice_launch/multiservice_launch.py
examples/A_service_and_entitycore/obi_one_entity_tools/entitysdk_example.ipynb
examples/A_service_and_entitycore/test_endpoints/test_endpoints.ipynb
examples/B_blocks/afferent_synapse_set_example.ipynb
examples/B_blocks/morphology_locations_example.ipynb
examples/B_blocks/motif_neuron_set_example.ipynb
examples/B_blocks/neuron_set_example.ipynb
examples/C_forms/basic_connectivity_plots/basic_connetivity_plots_example.ipynb
examples/C_forms/basic_connectivity_plots/colors_tab10.csv
examples/C_forms/circuit_extraction/circuit_extraction_example.ipynb
examples/C_forms/circuit_simulation/circuit_simulations_example.ipynb
examples/C_forms/circuit_simulation/circuit_simulations_with_manipulations_example.ipynb
examples/C_forms/connectivity_matrix_extraction/connectivity_matrix_extraction_example.ipynb
examples/C_forms/validation/reconstruction_morphology_validation_example.ipynb
examples/D_blueetl_example/analysis_config_01_relative_with_soma.yaml
examples/D_blueetl_example/blueetl_example.ipynb
examples/E_run_small_microcircuit/README.md
examples/E_run_small_microcircuit/run_circuit_bluecellab.py
examples/E_run_small_microcircuit/run_circuit_bluecellulab.sh
examples/E_run_small_microcircuit/run_circuit_simulation.ipynb
examples/F_single_cell_simulations/README.md
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examples/F_single_cell_simulations/calculate_threshold_holding.py
examples/F_single_cell_simulations/create_nodes_file.py
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examples/F_single_cell_simulations/components/circuit_config.json
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examples/F_single_cell_simulations/components/morphologies/C060114A5.asc
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examples/data/blueetl_data/analysis/analysis_config_01_relative.yaml
examples/data/blueetl_data/circuit/README
examples/data/blueetl_data/circuit/sonata/circuit_config.json
examples/data/blueetl_data/circuit/sonata/node_sets.json
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examples/data/single_neuron_circuits/SingleNeuronCircuit__top_nodes_dim6__IDX0/circuit_config.json
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examples/data/tiny_circuits/nbS1-O1-E2Sst-maxNsyn-HEX0-L5/morphologies/swc/rp110127_L5-2_idD_-_Clone_1.swc
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obi_one/database/__init__.py
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obi_one/scientific/basic_connectivity_plots/__init__.py
obi_one/scientific/basic_connectivity_plots/basic_connectivity_plots.py
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obi_one/scientific/circuit/__init__.py
obi_one/scientific/circuit/circuit.py
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obi_one/scientific/morphology_containerization/cell_template_neurodamus.jinja2
obi_one/scientific/morphology_containerization/cell_template_neurodamus_obi.jinja2
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obi_one/scientific/unions/unions_recordings.py
obi_one/scientific/unions/unions_stimuli.py
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projects/EM_circuits/morphology_containerization.ipynb
projects/EM_circuits/patch_edge_files.ipynb
projects/circuits_for_explore/basic_plots_all_connectomes.py
projects/circuits_for_explore/basic_plots_all_small_connectomes.py
projects/circuits_for_explore/circuit_extraction.ipynb
projects/circuits_for_explore/connectivity_matrix_extraction.ipynb
projects/circuits_for_explore/folder_compression.ipynb
projects/circuits_for_explore/morphology_containerization.ipynb
projects/circuits_for_explore/nodeset_generator.py
projects/circuits_for_explore/tests/circuit_extraction_test.ipynb
projects/circuits_for_explore/tests/connectivity_matrix_extraction_test.ipynb
projects/circuits_for_explore/tests/folder_compression_test.ipynb
projects/circuits_for_explore/tests/morphology_containerization_dev.ipynb
projects/circuits_for_explore/tests/morphology_containerization_test.ipynb
projects/tiny_circuits/Top10CentralNeurons_Layer_Hex.pkl
projects/tiny_circuits/Top10CentralNeurons_Layer_Hex_OptIDX.pkl
projects/tiny_circuits/check_mod_files.ipynb
projects/tiny_circuits/circuit_extraction.ipynb
projects/tiny_circuits/circuit_extraction_hippocampus.ipynb
projects/tiny_circuits/circuit_extraction_motif.ipynb
projects/tiny_circuits/circuit_extraction_simplex.ipynb
projects/tiny_circuits/circuit_extraction_volumetric.ipynb
projects/tiny_circuits/circuit_simulations.ipynb
projects/tiny_circuits/connectivity_matrix_extraction.ipynb
projects/tiny_circuits/folder_compression.ipynb
projects/tiny_circuits/hippocampus_cylinder_example.ipynb
projects/tiny_circuits/morphology_decontainerization.ipynb
projects/tiny_circuits/patch_circuits.ipynb
projects/tiny_circuits/selection1.csv
projects/tiny_circuits/selection2.csv
projects/tiny_circuits/single_neuron_extraction.ipynb
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tests/data/S1FL_L5_DBC_cIR_4.nwb
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