# 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¶

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:

• 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