Class NeuroMLBridge

java.lang.Object
org.episteme.natural.biology.loaders.neuroml.NeuroMLBridge
public class NeuroMLBridge extends Object
Bridge for converting NeuroML DTOs to core Episteme domain objects.

This bridge provides systematic conversion from NeuroML-parsed data transfer objects to the core Episteme architecture, enabling deep integration with the library's domain models for cells, neurons, synapses, and neural networks.

Architecture

NeuroML XML → NeuroMLReader → Cell/Morphology DTOs → NeuroMLBridge → Core Episteme Objects
                                                                     ├── Neuron
                                                                     ├── NeuronMorphology  
                                                                     ├── Synapse
                                                                     └── NeuralNetwork

Usage Example

NeuroMLReader reader = new NeuroMLReader();
NeuroMLModel model = reader.read(new File("neuron.nml"));

// Convert to core Episteme structures
NeuroMLBridge bridge = new NeuroMLBridge();
List<Neuron> neurons = bridge.toNeurons(model);
NeuralNetwork network = bridge.toNeuralNetwork(model);
Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)
See Also:

  • Constructor Details

    • NeuroMLBridge

      public NeuroMLBridge()

  • Method Details

    • toNeurons

      public List<Neuron> toNeurons(NeuroMLDocument model)
      Converts NeuroML Cell DTOs to Episteme Neuron objects.

      NeuroML cells contain morphological and biophysical data that maps to the neuroscience domain model.

      Parameters:
      model - the parsed NeuroML model
      Returns:
      list of Neuron objects

    • convertToNeuron

      public Neuron convertToNeuron(Cell neuromlCell)
      Converts a single NeuroML Cell DTO to a Episteme Neuron.
      Parameters:
      neuromlCell - the NeuroML cell DTO
      Returns:
      a Neuron, or null if conversion fails

    • convertMorphology

      public NeuronMorphology convertMorphology(Morphology morphology)
      Converts NeuroML Morphology to Episteme NeuronMorphology.
      Parameters:
      morphology - the NeuroML morphology DTO
      Returns:
      a NeuronMorphology object

    • toNeuralNetwork

      public NeuralNetwork toNeuralNetwork(NeuroMLDocument model)
      Converts NeuroML network to Episteme NeuralNetwork.
      Parameters:
      model - the parsed NeuroML model
      Returns:
      a NeuralNetwork containing populations and projections

    • toBiologyCell

      public Cell toBiologyCell(Cell neuromlCell)
      Converts a NeuroML Cell to a generic Episteme biology Cell.

      This provides a more basic conversion when full Neuron features are not needed.

      Parameters:
      neuromlCell - the NeuroML cell DTO
      Returns:
      a biology Cell object