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

Run Simulations¶

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 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

• 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]

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

  

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

    

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)

    

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

    

• 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

  

View Simulations¶

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

  • queue

  • aborted

  • failed

• 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

    

  • 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

    

• Delete the simulation

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