.. _syn_events_fit_user_data:

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Synaptic events fitting with user data
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This Use Case allows a user to fit data of synaptic events models from the 
NeuroInformatics Platform.

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 with user data - Config
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It allows the user to:

1. Select a local experimental file

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At this time, the only accepted format for the experimental file is a text file 
with time in the first column and individual traces in successive columns. 
All columns must be of the same length.

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2. Fill in the form with the values needed to write a configuration file: 
   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 vatiation range, 
   exclusion rules, and an optional set of dependencies for other parameters 
   are by default those corresponding to the model from the
   NeuroInformatics Platform

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    .. image:: images/fill_form.png
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    .. image:: images/fitting_params.png
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    .. image:: images/dependencies.png
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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), and check the job status.

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

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

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The user needs to be aware of the limitations imposed by each HPC system on resources

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On NSG the number of nodes, number of cores and the runtime are set by 
default to 2, 24 and 0.5 respectively. The maximum number of nodes available 
per job is 72. If you 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_02.png
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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, the user can see the 
submission date converted to CET time, next to the status of the job. This 
will be useful in the analysis notebook in order to fetch the job.

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

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

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5. If you want to start a new fitting from the beginning, click on the 
   “Click here to start a new fit” button.

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