.. _syn_events_fit:

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Synaptic events fitting
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This Use Case allows a user to fit synaptic events using data and models from the CSCS storage.

Selecting this Use Case, two Jupyter Notebooks are cloned in a private existing/new Collab.
The cloned Notebooks are:

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Synaptic events fitting - Config
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It allows the user to:

1. Select, download and visualize experimental data from the CSCS storage. The user may then select the data to be fitted.

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     .. image:: images/data_selection.png
         :width: 850px
         :align: center

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A configuration file corresponding to the selected experimental file is 
downloaded from the Collab storage. This file includes: the number of traces 
in the experimental file, the protocol (voltage clamp amplitude and reversal 
potential of the synapse), the name of the parameters to be fitted, their 
initial values and the allowed variation range, exclusion rules, and an optional 
set of dependencies for other parameters

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2. Select a default or a local mod file

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    .. image:: images/mod_selection.png
        :width: 300px
        :align: center

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We assume that the user knows what we are talking about here, and that the 
uploaded mod file has been already tested by the user in preliminary 
simulations. The program does not check this. An invalid file will result in 
errors at NEURON compilation time

When a local mod file is chosen, a form with the values needed to write a 
corresponding configuration file is opened. The number of traces in the 
experimental file and the protocol (voltage clamp amplitude and reversal 
potential of the synapse) are by default filled with the values corresponding 
to the chosen experimental file. The name of the parameters to be fitted, their 
initial values and allowed variation range, exclusion rules, and an optional 
set of dependencies for other parameters must be filled in by the user. Typical 
values are shown in the figures below:

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    .. image:: images/local_mod.png
        :width: 300px
        :align: center

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    .. image:: images/local_mod_values.png
        :width: 300px
        :align: center

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    .. image:: images/local_mod_values_params.png
        :width: 500px
        :align: center

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All other parameters that are not fitted have their default value as defined in the mod file.

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3. Configure the parameters of the optimization job: the title of the job, the number of nodes, the number of cores and the runtime. Run the fitting procedure using UNICORE authentication on JURECA (booster partition), GALILEO, or on NSG (using your account or the Service Account), and check the job status.

On JURECA, the node number, the number of CPUs per node and the runtime are set by default to 2, 24 and 10m respectively.

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On GALILEO, the node number, the number of CPUs per node and the runtime are set by default to 2, 36 and 10m respectively.

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The user needs to be aware of resource limitations imposed by each HPC system.

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On NSG, the node number, the number of cores and the runtime are set by 
default to 2, 24 and 0.5 (hours) respectively. The maximum node number per job 
is 72. If you would require more than 72 nodes, please contact 
nsghelp@sdsc.edu. The maximum number of cores required per node is 24.

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    .. image:: images/submission_process.png
        :width: 650px
        :align: center

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Note that when the job is submitted through UNICORE, the user can specify the project to use to submit the job on the HPC.

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 .. image:: images/unicore.png
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Note that when the job is submitted through NSG, next to the status of the job, the user may see the submission date converted to CET time. It will be useful in the analysis notebook in order to fetch the job.

The user can choose to fit all the experimental traces 100 times, a single trace 20 times or a demo version where a trace is fitted 5 times. For the single trace and the demo version the user can choose the number of the trace to be fitted.

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Once the job is completed, the output files will be in the Collab storage under different directories, according to the system used.

JURECA: results are saved under the resultsJureca/jobtitle_fitting_submissionTime folder.

GALILEO: results are saved under the resultsGalileo/jobtitle_fitting_submissionTime folder.

NSG results are saved under the resultsNSG/jobtitle_fitting_submissionTime folder.

NSG (Service Account) results are saved under the resultsNSG-SA/jobtitle_fitting_submissionTime folder.

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4. If you are interested in looking at the code, click on “Click here to toggle on/off the source code” button.

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    .. image:: images/toggle_button.png
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5. If you want to start a new fitting from the beginning, click on “Click here to start a new fit” button.

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    .. image:: images/Restart.png
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Synaptic events fitting - Analysis
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.. include:: ../syn_events_fit_analysis/syn_events_fit_analysis.rst