Simulation: Circuit simulation with Neuron

This project is a collaboration of scientists working in two HBP Subprojects:

  • Brain Simulation Platform (SP6)
  • HPAC Platform (SP7)


This use case consists of the following six steps:

  1. Creation of a circuit on a supercomputer.
  2. Release of this circuit: the data is visible to the HBP community through the Collaboratory.
  3. A user from another group configures a Neuron simulation based on the circuit model in the Collaboratory.
  4. The user launches the simulation from the Collaboratory.
  5. The user analyses the simulation results:
    1. With a predefined analysis that is available in a Collab, and/or
    2. By writing an own analysis, and/or
      • Writing and committing the analysis
      • Defining the dependencies
      • Selecting this newly defined analysis in the Collab
      • Selecting the simulation results in the Collab
      • Selecting the target system and job requirements
    3. By performing an interactive analysis using a notebook in the Collaboratory.
      • Launching a notebook from the Collaboratory that has access to the simulation reports and that has some predefined installed software
      • Executing the Python commands from the notebook that access the simulation reports
      • Saving the notebook
  6. The user launches the simulation reports and analysis in the Collaboratory to make the results available and reproducible.

Problems to be solved

The following problems require special attention and need to be solved in co-design with the users for implementing the use case successfully.

  • Provenance tracking of the entire, complex workflow is needed in order to enable reproducibility.
  • Visualisation of the simulation results.
  • A seamless integration with the Collaboratory is required to run the workflow from this portal, which in particular requires submitting and managing HPC jobs.