Configure and run a rat hippocampus CA1 region using preconfigured HBP model and data

This use case allows a user to configure and launch a simulation on HBP HPAC infrastructure using Unicore API.

Run Simulations

run_simulation

In the Section 1) you can configure:

  • Population: Population of cells to be loaded by the simulator.
  • Duration: Time length of stimulus duration, given in milliseconds(ms)
  • View Simulations: From here you can see all the history of simulations (explained in page View Simulations)

In the Section 2) you can configure:

  • Using the buttons edit_buttons you can add, edit or remove new stimulus/report (You can also double-click on the timeline to add or edit)
  • Stimulations configuration:
  • Population: Name of a population to receive the stimulation
  • Delay: Time when the stimulus commences, given in milliseconds(ms)
  • Duration: Time length of stimulus duration, given in milliseconds(ms)
  • Pattern: Type of stimulus to inject
  • Synapses per cell: The number of synapses to create
  • Lambda: Configure the random distribution
  • Weight: The strength of the created synapses
edit_stimulus
  • Reports
  • Population: Defines the population from where the data will be reported.
  • StartTime: Time to start reporting(ms)
  • EndTime: Time to stop reporting(ms)
  • Compartments: Which compartment(s) to report [Soma = compartment, Soma + Dendrites = AllCompartments]
  • ReportOn: What to report [Voltage, Calcium Concentration, Current Summation (for LFP)]
  • dt: The frequency of reporting in milliseconds(ms)
  • Format: Defines the report output format [Binary (.bbp), ASCII, HDF5]
edit_report

In the Section 3) you can modify the connection between populations on the circuit specifying:

  • Source: This target defines presynaptic cells

  • Destination: This target defines postsynaptic cells

  • Delay (ms): A delay after which the modifications are applied

  • Weight: A scaling factor to adjust the synaptic strength (default = 1)

  • MinisFreq: The Poisson mean rate for spontaneous synaptic activity

  • Synapse Configuration: Snippets of hoc code to manipulate additional synaptic parameters

    connection_manipulation

    • If you want to modify a synpase just click configure and a pop-up will appear

      synapse_configurator

In the Section 4) you can modify the projection going to the circuit

  • Weight: A scaling factor to adjust the synaptic strength (default = 1)

  • Minis Projection: Generate inputs based on spontaneous synaptic activity - Frequency (Hz): Frequency of the spontaneous synaptic activity

  • Spike Replay Projection: Generate inputs based on a given distribution

    • Target: From which cells the projection is coming

    • Frequency (Hz): The input mean rate

    • Stimulus Type: Type of distribution (default = Poisson)

      projection_manipulation

    • If you want to modify a projection just click configure and a pop-up will appear

      projection_edition

  • Launching a simulation will open a form to configure the parameters before executing the jobs on the supercomputer

  • Title: The title of the job

  • Computer: Which supercomputer will run the simulation.

  • Project: (optional) If you want to specify under which project the simulation should be run

  • Nodes: The amount of nodes that will be allocated and used for the simulation

  • Run Time: The maximum time before timeout (in seconds).

  • CPUs Per Node: Number of CPUs that are going to be used for the simulation.

  • Total Processors: The total amount (nodes * cpus).

  • Preview BlueConfig: This will open a new tab with the complete configuration that is going to be sent

    run_simulation_form


View Simulations

view_simulation

In the Section 1) you are able to:

  • Filter by Title, Status, Supercomputer, Project
  • Import Simulation providing the full path to simulation folder on that HPC
  • Launch Simulation: this goes back to Configure and Launch simuation page

In the Section 2) you are able to:

  • Check status of Simulation and Analysis steps:

    • ready done
    • queue sync
    • aborted block
    • failed error
  • View the details page of the simulation.

  • Analyse will open a form to configure the parameters before executing the analysis on the supercomputer

    • Title: Title of the job

    • Report: Report created by the simulation

    • Raster / Traces: (Basic Analysis) Type of analysis to run
      • Whole Population: Population cells
      • Cells GIDs: Specify single GID and/or ranges of GIDs
      • Random Cells: Amount of random cells (from the report) to analyze

      run_analysis_form

    • LFP: (Advanced Analysis) Type of analysis to run
      • Population: Population cells
      • Plots: Type of plots to get as a result of the LFP calculation
      • Duration: Start and End duration of the LFP calculation
      • Points: Either write or upload a file with points to calculate LFP

      run_lfp_analysis_form

  • Delete the simulation


Simulation Details

simulation_details

In the Section 1) you are able to see:

  • Simulation with the following information
    • Name
    • ID
    • Status
    • Submission Date

In the Section 2) you are able to see:

  • Analysis: Plots of the analysis will be shown here
  • BlueConfig: The configuration that was sent to run the simulation
  • Files: List of files that the simulation produced
  • Technical Logs:
    • Unicore Logs
    • Stderr: Logs of the simulation
    • Stdout: Output information of the simulation

The Analysis section shows the different analyses the user has run

simulation_details_analysis