Wiki source code of Simulate with EBRAINS Workshop, Nov 2022
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| 5 | = Welcome = | ||
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| 7 | This shared workspace (or "collab") is for participants in the [[HBP Young Researchers Event 2022>>https://www.humanbrainproject.eu/en/education/YRE2022-Denmark/||rel="noopener noreferrer" target="_blank"]] in Copenhagen who are taking part in the hands-on session "Using the PyNN library to build and simulate models on EBRAINS". | ||
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| 9 | 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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| 11 | Since it is hands-on, each participant should work on their own laptop with their own copy of the notebook. If you'd prefer to work in small groups of 2 or 3 round a single laptop, that's also fine. | ||
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| 13 | 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. | ||
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| 15 | = Resources = | ||
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| 17 | * [[Rocket chat channel>>https://chat.ebrains.eu/channel/PyNN||rel="noopener noreferrer" target="_blank"]] for asking questions during or after the session | ||
| 18 | * [[PyNN documentation>>http://neuralensemble.org/docs/PyNN/||rel="noopener noreferrer" target="_blank"]] | ||
| 19 | * PyNN tutorials on YouTube | ||
| 20 | ** [[Installing PyNN on a Linux system>>https://www.youtube.com/watch?v=Ui8_I9T0UcU||rel="noopener noreferrer" target="_blank"]] | ||
| 21 | ** [[Building and simulating a simple model using PyNN>>https://www.youtube.com/watch?v=azBQRXMsLPY||rel="noopener noreferrer" target="_blank"]] | ||
| 22 | * [[Collaboratory documentation>>https://wiki.ebrains.eu/bin/view/Collabs/the-collaboratory/||rel="noopener noreferrer" target="_blank"]] | ||
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| 24 | = Instructions = | ||
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| 26 | 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". | ||
| 27 | 1. Copy the Jupyter notebook to your own collab | ||
| 28 | 11. (option A) click [[here>>https://collab-file-cloner.netlify.app/#source_file=https://drive.ebrains.eu/f/98f1bc8e294040a4a8f9/&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". | ||
| 29 | 11. (option B) in this collab, click on "Drive". Next to "PyNN_tutorial.ipynb" click on the "more options" button, then "Copy". In "Other Libraries" select your own collab then click "Submit". | ||
| 30 | 1. In your own collab, click on Lab, then select either "Fenix CH" or "Fenix DE". | ||
| 31 | 1. On the "Server Options" page, select "Official EBRAINS Docker image 22.03 for Collaboratory.Lab" then click "Start". | ||
| 32 | 1. In the left-hand file chooser, double-click on "PyNN_tutorial.ipynb". | ||
| 33 | 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>" | ||
| 34 | ))) | ||
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| 39 | {{box title="**Contents**"}} | ||
| 40 | {{toc/}} | ||
| 41 | {{/box}} | ||
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| 44 | ))) | ||
| 45 | ))) |