diff --git a/api/spec/openapi_3_1_0_generated.yaml b/api/spec/openapi_3_1_0_generated.yaml
new file mode 100644
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+++ b/api/spec/openapi_3_1_0_generated.yaml
@@ -0,0 +1,923 @@
+openapi: 3.1.0
+info:
+  title: bio-compose
+  version: 1.12.0
+paths:
+  /:
+    get:
+      summary: Root
+      operationId: root__get
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+  /run-smoldyn:
+    post:
+      tags:
+      - Simulation Execution
+      summary: Run a smoldyn simulation.
+      operationId: run-smoldyn
+      parameters:
+      - name: duration
+        in: query
+        required: false
+        schema:
+          type: integer
+          description: Simulation Duration
+          title: Duration
+        description: Simulation Duration
+      - name: dt
+        in: query
+        required: false
+        schema:
+          type: number
+          description: Interval of step with which simulation runs
+          title: Dt
+        description: Interval of step with which simulation runs
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_run-smoldyn'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/SmoldynRun'
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /run-utc:
+    post:
+      tags:
+      - Simulation Execution
+      summary: Run a Uniform Time Course simulation.
+      operationId: run-utc
+      parameters:
+      - name: start
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: Starting time for utc
+          title: Start
+        description: Starting time for utc
+      - name: end
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: Simulation Duration
+          title: End
+        description: Simulation Duration
+      - name: steps
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: Number of points for utc
+          title: Steps
+        description: Number of points for utc
+      - name: simulator
+        in: query
+        required: true
+        schema:
+          type: string
+          description: 'Simulator to use (one of: amici, copasi, tellurium, vcell)'
+          title: Simulator
+        description: 'Simulator to use (one of: amici, copasi, tellurium, vcell)'
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_run-utc'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /verify-omex:
+    post:
+      tags:
+      - Verification
+      summary: Compare UTC outputs from a deterministic SBML model within an OMEX/COMBINE
+        archive.
+      operationId: verify-omex
+      parameters:
+      - name: simulators
+        in: query
+        required: false
+        schema:
+          type: array
+          items:
+            type: string
+          description: List of simulators to compare
+          default:
+          - amici
+          - copasi
+          - pysces
+          - tellurium
+          title: Simulators
+        description: List of simulators to compare
+      - name: include_outputs
+        in: query
+        required: false
+        schema:
+          type: boolean
+          description: Whether to include the output data on which the comparison
+            is based.
+          default: true
+          title: Include Outputs
+        description: Whether to include the output data on which the comparison is
+          based.
+      - name: selection_list
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: array
+            items:
+              type: string
+          - type: 'null'
+          description: List of observables to include in the return data.
+          title: Selection List
+        description: List of observables to include in the return data.
+      - name: comparison_id
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: string
+          - type: 'null'
+          description: Descriptive prefix to be added to this submission's job ID.
+          title: Comparison Id
+        description: Descriptive prefix to be added to this submission's job ID.
+      - name: rTol
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: number
+          - type: 'null'
+          description: Relative tolerance to use for proximity comparison.
+          title: Rtol
+        description: Relative tolerance to use for proximity comparison.
+      - name: aTol
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: number
+          - type: 'null'
+          description: Absolute tolerance to use for proximity comparison.
+          title: Atol
+        description: Absolute tolerance to use for proximity comparison.
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_verify-omex'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/OmexVerificationRun'
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /verify-sbml:
+    post:
+      tags:
+      - Verification
+      summary: Compare UTC outputs from a deterministic SBML model.
+      operationId: verify-sbml
+      parameters:
+      - name: start
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: Start time of the simulation (output start time)
+          title: Start
+        description: Start time of the simulation (output start time)
+      - name: end
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: End time of simulation (end)
+          title: End
+        description: End time of simulation (end)
+      - name: steps
+        in: query
+        required: true
+        schema:
+          type: integer
+          description: Number of simulation steps to run
+          title: Steps
+        description: Number of simulation steps to run
+      - name: simulators
+        in: query
+        required: false
+        schema:
+          type: array
+          items:
+            type: string
+          description: List of simulators to compare
+          default:
+          - amici
+          - copasi
+          - pysces
+          - tellurium
+          title: Simulators
+        description: List of simulators to compare
+      - name: include_outputs
+        in: query
+        required: false
+        schema:
+          type: boolean
+          description: Whether to include the output data on which the comparison
+            is based.
+          default: true
+          title: Include Outputs
+        description: Whether to include the output data on which the comparison is
+          based.
+      - name: comparison_id
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: string
+          - type: 'null'
+          description: Descriptive prefix to be added to this submission's job ID.
+          title: Comparison Id
+        description: Descriptive prefix to be added to this submission's job ID.
+      - name: rTol
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: number
+          - type: 'null'
+          description: Relative tolerance to use for proximity comparison.
+          title: Rtol
+        description: Relative tolerance to use for proximity comparison.
+      - name: aTol
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: number
+          - type: 'null'
+          description: Absolute tolerance to use for proximity comparison.
+          title: Atol
+        description: Absolute tolerance to use for proximity comparison.
+      - name: selection_list
+        in: query
+        required: false
+        schema:
+          anyOf:
+          - type: array
+            items:
+              type: string
+          - type: 'null'
+          description: List of observables to include in the return data.
+          title: Selection List
+        description: List of observables to include in the return data.
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_verify-sbml'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/SbmlVerificationRun'
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /get-smoldyn-output/{job_id}:
+    get:
+      tags:
+      - Results
+      summary: Get the results of an existing Smoldyn simulation run as either a downloadable
+        file or job progression status.
+      operationId: get-smoldyn-output
+      parameters:
+      - name: job_id
+        in: path
+        required: true
+        schema:
+          type: string
+          title: Job Id
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /get-verification-output/{job_id}:
+    get:
+      tags:
+      - Results
+      summary: Get the results of an existing verification run.
+      operationId: get-verification-output
+      parameters:
+      - name: job_id
+        in: path
+        required: true
+        schema:
+          type: string
+          title: Job Id
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/VerificationOutput'
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /get-output/{job_id}:
+    get:
+      tags:
+      - Results
+      summary: Get the results of an existing simulation run.
+      operationId: get-output
+      parameters:
+      - name: job_id
+        in: path
+        required: true
+        schema:
+          type: string
+          title: Job Id
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /generate-simularium-file:
+    post:
+      tags:
+      - Files
+      summary: Generate a simularium file with a compatible simulation results file
+        from either Smoldyn, SpringSaLaD, or ReaDDy.
+      operationId: generate-simularium-file
+      parameters:
+      - name: box_size
+        in: query
+        required: true
+        schema:
+          type: number
+          description: Size of the simulation box as a floating point number.
+          title: Box Size
+        description: Size of the simulation box as a floating point number.
+      - name: filename
+        in: query
+        required: false
+        schema:
+          type: string
+          description: 'Name desired for the simularium file. NOTE: pass only the
+            file name without an extension.'
+          title: Filename
+        description: 'Name desired for the simularium file. NOTE: pass only the file
+          name without an extension.'
+      - name: translate_output
+        in: query
+        required: false
+        schema:
+          type: boolean
+          description: Whether to translate the output trajectory prior to converting
+            to simularium. See simulariumio documentation for more details.
+          default: true
+          title: Translate Output
+        description: Whether to translate the output trajectory prior to converting
+          to simularium. See simulariumio documentation for more details.
+      - name: validate_output
+        in: query
+        required: false
+        schema:
+          type: boolean
+          description: Whether to validate the outputs for the simularium file. See
+            simulariumio documentation for more details.
+          default: true
+          title: Validate Output
+        description: Whether to validate the outputs for the simularium file. See
+          simulariumio documentation for more details.
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_generate-simularium-file'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema: {}
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+  /get-compatible-for-verification:
+    post:
+      tags:
+      - Files
+      summary: Get the simulators that are compatible with either a given OMEX/COMBINE
+        archive or SBML model simulation.
+      operationId: get-compatible-for-verification
+      parameters:
+      - name: versions
+        in: query
+        required: false
+        schema:
+          type: boolean
+          description: Whether to include the simulator versions for each compatible
+            simulator.
+          default: false
+          title: Versions
+        description: Whether to include the simulator versions for each compatible
+          simulator.
+      requestBody:
+        required: true
+        content:
+          multipart/form-data:
+            schema:
+              $ref: '#/components/schemas/Body_get-compatible-for-verification'
+      responses:
+        '200':
+          description: Successful Response
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/CompatibleSimulators'
+        '422':
+          description: Validation Error
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/HTTPValidationError'
+components:
+  schemas:
+    AgentParameter:
+      properties:
+        name:
+          type: string
+          title: Name
+        radius:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Radius
+        mass:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Mass
+        density:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Density
+      type: object
+      required:
+      - name
+      - radius
+      - mass
+      - density
+      title: AgentParameter
+    AgentParameters:
+      properties:
+        agents:
+          items:
+            $ref: '#/components/schemas/AgentParameter'
+          type: array
+          title: Agents
+      type: object
+      required:
+      - agents
+      title: AgentParameters
+    Body_generate-simularium-file:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: A file containing results that can be parse by Simularium (spatial).
+        agent_parameters:
+          $ref: '#/components/schemas/AgentParameters'
+          description: Parameters for the simularium agents defining either radius
+            or mass and density.
+      type: object
+      required:
+      - uploaded_file
+      title: Body_generate-simularium-file
+    Body_get-compatible-for-verification:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: Either a COMBINE/OMEX archive or SBML file to be simulated.
+      type: object
+      required:
+      - uploaded_file
+      title: Body_get-compatible-for-verification
+    Body_run-smoldyn:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: Smoldyn Configuration File
+      type: object
+      required:
+      - uploaded_file
+      title: Body_run-smoldyn
+    Body_run-utc:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: SBML File
+      type: object
+      required:
+      - uploaded_file
+      title: Body_run-utc
+    Body_verify-omex:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: OMEX/COMBINE archive containing a deterministic SBML model
+      type: object
+      required:
+      - uploaded_file
+      title: Body_verify-omex
+    Body_verify-sbml:
+      properties:
+        uploaded_file:
+          type: string
+          format: binary
+          title: Uploaded File
+          description: A deterministic SBML model.
+      type: object
+      required:
+      - uploaded_file
+      title: Body_verify-sbml
+    CompatibleSimulators:
+      properties:
+        file:
+          type: string
+          title: File
+        simulators:
+          items:
+            $ref: '#/components/schemas/Simulator'
+          type: array
+          title: Simulators
+      type: object
+      required:
+      - file
+      - simulators
+      title: CompatibleSimulators
+    HTTPValidationError:
+      properties:
+        detail:
+          items:
+            $ref: '#/components/schemas/ValidationError'
+          type: array
+          title: Detail
+      type: object
+      title: HTTPValidationError
+    ObservableData:
+      properties:
+        observable_name:
+          type: string
+          title: Observable Name
+        mse:
+          type: object
+          title: Mse
+        proximity:
+          type: object
+          title: Proximity
+        output_data:
+          additionalProperties:
+            anyOf:
+            - items:
+                type: number
+              type: array
+            - type: string
+          type: object
+          title: Output Data
+      type: object
+      required:
+      - observable_name
+      - mse
+      - proximity
+      - output_data
+      title: ObservableData
+    OmexVerificationRun:
+      properties:
+        job_id:
+          type: string
+          title: Job Id
+        timestamp:
+          type: string
+          title: Timestamp
+        status:
+          type: string
+          title: Status
+        path:
+          type: string
+          title: Path
+        simulators:
+          items:
+            type: string
+          type: array
+          title: Simulators
+        include_outputs:
+          anyOf:
+          - type: boolean
+          - type: 'null'
+          title: Include Outputs
+          default: true
+        selection_list:
+          anyOf:
+          - items:
+              type: string
+            type: array
+          - type: 'null'
+          title: Selection List
+        comparison_id:
+          anyOf:
+          - type: string
+          - type: 'null'
+          title: Comparison Id
+        rTol:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Rtol
+        aTol:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Atol
+      type: object
+      required:
+      - job_id
+      - timestamp
+      - status
+      - path
+      - simulators
+      title: OmexVerificationRun
+    SbmlVerificationRun:
+      properties:
+        job_id:
+          type: string
+          title: Job Id
+        timestamp:
+          type: string
+          title: Timestamp
+        status:
+          type: string
+          title: Status
+        path:
+          type: string
+          title: Path
+        simulators:
+          items:
+            type: string
+          type: array
+          title: Simulators
+        include_outputs:
+          anyOf:
+          - type: boolean
+          - type: 'null'
+          title: Include Outputs
+          default: true
+        selection_list:
+          anyOf:
+          - items:
+              type: string
+            type: array
+          - type: 'null'
+          title: Selection List
+        comparison_id:
+          anyOf:
+          - type: string
+          - type: 'null'
+          title: Comparison Id
+        rTol:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Rtol
+        aTol:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Atol
+        start:
+          type: integer
+          title: Start
+        end:
+          type: integer
+          title: End
+        steps:
+          type: integer
+          title: Steps
+      type: object
+      required:
+      - job_id
+      - timestamp
+      - status
+      - path
+      - simulators
+      - start
+      - end
+      - steps
+      title: SbmlVerificationRun
+    Simulator:
+      properties:
+        name:
+          type: string
+          title: Name
+        version:
+          anyOf:
+          - type: string
+          - type: 'null'
+          title: Version
+      type: object
+      required:
+      - name
+      title: Simulator
+    SimulatorRMSE:
+      properties:
+        simulator:
+          type: string
+          title: Simulator
+        rmse_scores:
+          additionalProperties:
+            type: number
+          type: object
+          title: Rmse Scores
+      type: object
+      required:
+      - simulator
+      - rmse_scores
+      title: SimulatorRMSE
+    SmoldynRun:
+      properties:
+        job_id:
+          type: string
+          title: Job Id
+        timestamp:
+          type: string
+          title: Timestamp
+        status:
+          type: string
+          title: Status
+        path:
+          type: string
+          title: Path
+        simulators:
+          items:
+            type: string
+          type: array
+          title: Simulators
+          default:
+          - smoldyn
+        duration:
+          anyOf:
+          - type: integer
+          - type: 'null'
+          title: Duration
+        dt:
+          anyOf:
+          - type: number
+          - type: 'null'
+          title: Dt
+      type: object
+      required:
+      - job_id
+      - timestamp
+      - status
+      - path
+      title: SmoldynRun
+    ValidationError:
+      properties:
+        loc:
+          items:
+            anyOf:
+            - type: string
+            - type: integer
+          type: array
+          title: Location
+        msg:
+          type: string
+          title: Message
+        type:
+          type: string
+          title: Error Type
+      type: object
+      required:
+      - loc
+      - msg
+      - type
+      title: ValidationError
+    VerificationOutput:
+      properties:
+        job_id:
+          type: string
+          title: Job Id
+        timestamp:
+          type: string
+          title: Timestamp
+        status:
+          type: string
+          title: Status
+        source:
+          anyOf:
+          - type: string
+          - type: 'null'
+          title: Source
+        requested_simulators:
+          anyOf:
+          - items:
+              type: string
+            type: array
+          - type: 'null'
+          title: Requested Simulators
+        results:
+          anyOf:
+          - items:
+              anyOf:
+              - $ref: '#/components/schemas/ObservableData'
+              - $ref: '#/components/schemas/SimulatorRMSE'
+              - {}
+            type: array
+          - type: object
+          - type: 'null'
+          title: Results
+      type: object
+      required:
+      - job_id
+      - timestamp
+      - status
+      title: VerificationOutput
+      description: "Return schema for get-verification-output.\n\nParameters:\n  \
+        \  job_id: str\n    timestamp: str\n    status: str --> may be COMPLETE, IN_PROGRESS,\
+        \ FAILED, or PENDING\n    source: str\n    requested_simulators: List[str]\n\
+        \    results: Optional[dict] = None TODO: parse this"