Simulate with EBRAINS Workshop, Nov 2022

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= Welcome =

This wiki page is for participants in the "Simulate with EBRAINS" online workshop, 7-10 November 2022, who are taking part in the hands-on session "Using the PyNN library to build and simulate models on EBRAINS".

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In this hands-on session we will work together through a Jupyter notebook which demonstrates the basics of working with PyNN.

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This first page contains instructions for getting started with the hands-on session, and a list of resources for getting help and finding further documentation and tutorials.

= Resources =

* [[Rocket chat channel>>https://chat.ebrains.eu/channel/PyNN||rel="noopener noreferrer" target="_blank"]] for asking questions during or after the session

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* [[PyNN documentation>>http://neuralensemble.org/docs/PyNN/||rel="noopener noreferrer" target="_blank"]]

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* PyNN tutorials on YouTube

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** [[Installing PyNN on a Linux system>>https://www.youtube.com/watch?v=BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]]

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** [[Building and simulating a simple model using PyNN>>https://www.youtube.com/watch?v=zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]]

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* [[Collaboratory documentation>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/||rel="noopener noreferrer" target="_blank"]]

= Instructions =

1. So you can save any changes you might make to the notebook, it is best to work in your own collab workspace. If you already have a collab you want to use, open it in a new tab. If not, create a new one by clicking [[here>>https://wiki.ebrains.eu/bin/view/Collabs?clbaction=create||rel="noopener noreferrer" target="_blank"]] or clicking on "Collabs" in the top menu then "Create a collab".

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1. After creating a Collab, you need to initialise the Drive (file storage), by clicking on the Drive link in the left-hand column.

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1. Copy the Jupyter notebook to your own collab

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11. (option A) click [[here>>https://collab-file-cloner.netlify.app/#source_file=https://drive.ebrains.eu/f/cc1d63667c514435b26f//&file_overwrite=true&auto_run=true&open_lab=true||rel="noopener noreferrer" target="_blank"]], select "yes" in the "Grant Access to Collab File Cloner" dialog, select the target collab in the drop-down list, then click "Continue" followed by "Clone File".

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11. (option B) in this collab, click on "Drive", then "HandsOn" then "SimulateWithEBRAINS_Nov2022". Next to "PyNN_tutorial.ipynb" click on the "more options" button, then "Copy". In "Other Libraries" select your own collab then click "Submit".

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1. In your own collab, click on Lab, then select either "Fenix CH" or "Fenix DE".

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1. On the "Server Options" page, select "Official EBRAINS Docker image 22.03 for Collaboratory.Lab" then click "Start".

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1. In the left-hand file chooser, wait until the file listing appears (may take a few tens of seconds), then double-click on "PyNN_tutorial.ipynb".

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1. We will work through the notebook together, discussing each cell as we execute it. If you're not familiar with Jupyter notebooks, note that you can run a cell either by clicking the "play" icon or by typing "<shift>-<return>"

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Wiki source code of Simulate with EBRAINS Workshop, Nov 2022

PyNN: resources