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AurelienJaquiereleftherioszisis
AurelienJaquier
and
eleftherioszisis
authored
new ion channel modeling entities (#139)
* Ion channel models * Fix tests --------- Co-authored-by: Eleftherios Zisis <eleftherios.zisis@openbraininstitute.org>
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‎src/entitysdk/models/__init__.py‎

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from entitysdk.models.etype import ETypeClass
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from entitysdk.models.ion_channel import IonChannel
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from entitysdk.models.ion_channel_model import IonChannelModel, NeuronBlock, UseIon
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from entitysdk.models.ion_channel_modeling_campaign import IonChannelModelingCampaign
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from entitysdk.models.ion_channel_modeling_config import IonChannelModelingConfig
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from entitysdk.models.ion_channel_modeling_config_generation import (
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IonChannelModelingConfigGeneration,
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)
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from entitysdk.models.ion_channel_modeling_execution import IonChannelModelingExecution
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from entitysdk.models.ion_channel_recording import IonChannelRecording
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from entitysdk.models.license import License
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from entitysdk.models.measurement_annotation import MeasurementAnnotation
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"ETypeClassification",
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"IonChannel",
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"IonChannelModel",
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"IonChannelModelingCampaign",
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"IonChannelModelingConfig",
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"IonChannelModelingConfigGeneration",
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"IonChannelModelingExecution",
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"IonChannelRecording",
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"License",
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"MeasurementAnnotation",

‎src/entitysdk/models/ion_channel_modeling_campaign.py‎

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"""Ion channel modeling campaign model."""
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from entitysdk.models.entity import Entity
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from entitysdk.models.ion_channel_modeling_config import IonChannelModelingConfig
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from entitysdk.models.ion_channel_recording import IonChannelRecording
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class IonChannelModelingCampaign(Entity):
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"""IonChannelModelingCampaign model."""
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scan_parameters: dict
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ion_channel_modeling_configs: list[IonChannelModelingConfig] | None = None
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input_recordings: list[IonChannelRecording] | None = None

‎src/entitysdk/models/ion_channel_modeling_config.py‎

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"""Ion channel modeling config model."""
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from entitysdk.models.entity import Entity
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from entitysdk.types import ID
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class IonChannelModelingConfig(Entity):
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"""IonChannelModelingConfig model."""
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ion_channel_modeling_campaign_id: ID
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scan_parameters: dict

‎src/entitysdk/models/ion_channel_modeling_config_generation.py‎

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"""Ion channel modeling config generation model."""
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from entitysdk.models.activity import Activity
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class IonChannelModelingConfigGeneration(Activity):
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"""Ion channel modeling config generation activity class."""
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pass

‎src/entitysdk/models/ion_channel_modeling_execution.py‎

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"""Ion channel modeling execution model."""
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from entitysdk.models.activity import Activity
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from entitysdk.types import IonChannelModelingExecutionStatus
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class IonChannelModelingExecution(Activity):
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"""Ion channel modeling execution model."""
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status: IonChannelModelingExecutionStatus

‎src/entitysdk/route.py‎

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"Ion": "ion",
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"IonChannel": "ion-channel",
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"IonChannelModel": "ion-channel-model",
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"IonChannelModelingCampaign": "ion-channel-modeling-campaign",
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"IonChannelModelingConfig": "ion-channel-modeling-config",
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"IonChannelModelingConfigGeneration": "ion-channel-modeling-config-generation",
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"IonChannelModelingExecution": "ion-channel-modeling-execution",
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"IonChannelRecording": "ion-channel-recording",
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"License": "license",
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"MeasurementAnnotation": "measurement-annotation",

‎src/entitysdk/types.py‎

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from entitysdk._server_schemas import EMCellMeshGenerationMethod as EMCellMeshGenerationMethod
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from entitysdk._server_schemas import EMCellMeshType as EMCellMeshType
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from entitysdk._server_schemas import EntityType as EntityType
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from entitysdk._server_schemas import (
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IonChannelModelingExecutionStatus as IonChannelModelingExecutionStatus,
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)
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from entitysdk._server_schemas import MeasurableEntity as MeasurableEntity
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from entitysdk._server_schemas import MeasurementStatistic as MeasurementStatistic
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from entitysdk._server_schemas import MeasurementUnit as MeasurementUnit

‎tests/integration/test_searching.py‎

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EModel,
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IonChannel,
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IonChannelModel,
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IonChannelModelingCampaign,
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IonChannelModelingConfig,
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IonChannelModelingConfigGeneration,
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IonChannelModelingExecution,
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IonChannelRecording,
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License,
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MEModel,
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Contribution,
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IonChannel,
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IonChannelModel,
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IonChannelModelingCampaign,
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IonChannelModelingConfig,
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IonChannelModelingConfigGeneration,
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IonChannelModelingExecution,
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IonChannelRecording,
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License,
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MTypeClass,

‎tests/unit/models/data/ion_channel_modeling_campaign.json‎

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{
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"assets": [],
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"id": "be2daf30-c2a0-4433-a0e2-5e20ccff5908",
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"update_date": "2025-06-11T09:33:51.707275Z",
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"creation_date": "2025-06-11T09:33:51.707275Z",
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"name": "my-campaign",
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"description": "my-campaign-description",
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"type": "ion_channel_modeling_campaign",
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"scan_parameters": {"foo": "bar"},
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"input_recordings": [
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{
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"contributions": [],
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"assets": [
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{
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"size": 1657656,
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"creation_date": null,
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"sha256_digest": "96cc3960ce65133a79be19af9b8b5fa614eb42328cb2e4c67fbe0f96c51c28e2",
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"path": "S1FL_L5_DBC_cIR_4.nwb",
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"full_path": "public/a98b7abc-fc46-4700-9e3d-37137812c730/0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6/assets/electrical_cell_recording/98dece14-e154-4ff1-9c1d-34e1563cdd0a/S1FL_L5_DBC_cIR_4.nwb",
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"is_directory": false,
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"content_type": "application/nwb",
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"meta": {},
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"label": "nwb",
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"id": "898ef0f4-d36f-4426-8af7-145cdb202004",
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"storage_type": "aws_s3_internal",
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"status": "created"
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}
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],
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"license": {
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"id": "c268a20e-b78a-4332-a5e1-38e26c4454b9",
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"creation_date": "2025-06-27T11:10:28.715323Z",
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"update_date": "2025-06-27T11:10:28.715324Z",
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"name": "https://bbp.epfl.ch/neurosciencegraph/data/licenses/97521f71-605d-4f42-8f1b-c37e742a30bf",
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"description": "undefined",
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"label": "undefined"
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},
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"creation_date": "2021-06-15T09:42:25.311000Z",
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"update_date": "2024-01-11T07:56:56.842835Z",
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"created_by": {
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"id": "4067c358-4ee2-47f8-9a94-e3e8ab73738f",
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"given_name": "Anna-Kristin",
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"family_name": "Kaufmann",
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"pref_label": "Anna-Kristin Kaufmann",
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"type": "person",
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},
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"updated_by": {
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"id": "bd143fa9-b714-410c-a65d-7435c1066932",
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"given_name": "Christina",
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"family_name": "Gonzalez",
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"pref_label": "Christina Gonzalez",
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"type": "person",
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"creation_date": null,
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"update_date": null
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},
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"brain_region": {
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"creation_date": "2025-06-27T11:10:27.186088Z",
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"update_date": "2025-06-27T11:10:27.186088Z",
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"id": "61d89b07-dfa0-439a-9187-7ebfe60e212b",
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"annotation_value": 322,
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"name": "Primary somatosensory area",
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"acronym": "SSp",
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"color_hex_triplet": "188064",
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"parent_structure_id": "9680c40f-ccfe-4804-851f-1024ff0d6409",
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"hierarchy_id": "e3e70682-c209-4cac-a29f-6fbed82c07cd"
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},
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"subject": {
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"id": "9fb86d35-6bda-4b8d-9eb3-2715c98fff3b",
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"name": "Unknown",
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"description": "",
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"sex": "unknown",
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"weight": null,
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"age_value": null,
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"age_min": null,
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"age_max": null,
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"age_period": null,
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"species": {
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"id": "3b1c2a25-b4fb-468d-98d2-d2d431ac8b4a",
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"name": "Rattus norvegicus",
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"taxonomy_id": "NCBITaxon:10116",
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"creation_date": null,
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"update_date": null
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},
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"strain": null,
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"assets": [],
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"type": null,
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"authorized_public": false,
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},
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"authorized_project_id": "0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6",
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"authorized_public": true,
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"type": "ion_channel_recording",
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"id": "98dece14-e154-4ff1-9c1d-34e1563cdd0a",
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"experiment_date": null,
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"contact_email": null,
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"published_in": null,
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"name": "Cell 29414",
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"description": "Kv1.1 recording.",
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"ljp": 0.0,
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"recording_location": [],
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"recording_type": "intracellular",
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"recording_origin": "in_silico",
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"temperature": null,
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"comment": "RTR (30 min pre-incubation in HBSS)",
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"legacy_id": null,
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"stimuli": [
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{
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"assets": [],
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"authorized_project_id": null,
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"authorized_public": false,
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"contributions": null,
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"created_by": null,
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"type": "electrical_recording_stimulus",
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"id": "b487b0da-33dd-4cf1-a9c7-6d19a2b55ab7",
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"name": "GenericStep",
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"description": "",
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"dt": null,
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"injection_type": "current_clamp",
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"shape": "step",
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"start_time": null,
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"end_time": null,
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"recording_id": "98dece14-e154-4ff1-9c1d-34e1563cdd0a",
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},
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"type": "electrical_recording_stimulus",
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"injection_type": "current_clamp",
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"recording_id": "98dece14-e154-4ff1-9c1d-34e1563cdd0a"
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},
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{
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"type": "electrical_recording_stimulus",
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"id": "5d0664fd-7785-48e0-b760-532a73f59f14",
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"recording_id": "98dece14-e154-4ff1-9c1d-34e1563cdd0a"
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}
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],
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"cell_line": "CHO",
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"ion_channel": {
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"creation_date": "2021-06-15T09:42:25.311000Z",
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"update_date": "2024-01-11T07:56:56.842835Z",
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"id": "98dece14-e154-4ff1-9c1d-34e1563cdd0a",
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"label": "K<SUB>v<\/SUB>1.1",
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"gene": "Kcna1",
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"synonyms": ["HBK1", "Kcn1", "MBK1", "RCK1", "AEMK", "HUK1", "Shak", "Kcna", "Kcpvd"],
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"name": "Kv1.1",
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"description": ""
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}
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}
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],
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"id": "e8997b32-0183-42c8-b11f-1a61da933a89",
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"type": "person",
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"pref_label": "Admin User",
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},
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"id": "e8997b32-0183-42c8-b11f-1a61da933a89",
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"ion_channel_modeling_configs": [
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{
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"id": "32073304-a8cc-4461-9ef7-9d526527214b",
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"name": "ion-channel-modeling-config-0",
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"description": "ion-channel-modeling-config-0",
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"type": "ion_channel_modeling_config",
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"authorized_public": false,
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"ion_channel_modeling_campaign_id": "be2daf30-c2a0-4433-a0e2-5e20ccff5908",
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"scan_parameters": {
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"foo": "bar"
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}
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},
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{
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"assets": [],
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"id": "e2549cb6-c065-4827-ba09-005117a0a1a7",
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"name": "ion-channel-modeling-config-1",
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"description": "ion-channel-modeling-config-1",
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"type": "ion_channel_modeling_config",
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"ion_channel_modeling_campaign_id": "be2daf30-c2a0-4433-a0e2-5e20ccff5908",
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"scan_parameters": {
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"foo": "bar"
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}
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}
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]
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}

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