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Add a "Try this on EBRAINS" button for single-click installation-free setups #1

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8857777
Update and rename readme.org to readme.md
terhorstd Jun 21, 2024
4c6efbf
Update kernel in arbor-tutorial.ipynb
terhorstd Jun 21, 2024
b367530
Fix matplotlib inline output
terhorstd Jun 21, 2024
306b9e4
Fix kernel name
terhorstd Jun 24, 2024
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5 changes: 3 additions & 2 deletions arbor-tutorial.ipynb
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Expand Up @@ -24,6 +24,7 @@
"metadata": {},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import arbor as A\n",
"import numpy as np\n",
"import seaborn as sns\n",
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],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "EBRAINS-24.04",
"language": "python",
"name": "python3"
"name": "ebrains-24.04"
},
"language_info": {
"codemirror_mode": {
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22 changes: 13 additions & 9 deletions readme.org → readme.md
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@@ -1,28 +1,32 @@
#+title: Readme

* Arbor Tutorial for NestConf
# Arbor Tutorial for [NEST Conference 2024](https://nest-simulator.org/conference-2024)

This tutorial take you from the bare bones concepts of bio-physically detailled
cells to a simple network in Arbor. It is meant mainly for self-directed study
and experimentation with the opportunity to ask questions. If you are tackling
this on your own (i.e. not during a workshop), please contact us on [[https://app.gitter.im/#/room/#arbor-tutorial:gitter.im][Gitter]].
this on your own (i.e. not during a workshop), please contact us on [Gitter](https://app.gitter.im/#/room/#arbor-tutorial:gitter.im).

## Getting Started

The easiest way to run this tutorial is installation-free on the EBRAINS platform. You can open an account with your institutional email address for free and then start the tutorial here:

[![](https://nest-simulator.org/TryItOnEBRAINS.png)](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fthorstenhater%2Farbor-tutorial&urlpath=lab%2Ftree%2Farbor-tutorial%2Farbor-tutorial.ipynb&branch=main)

* Getting Started
Aternatively you can install all dependencies on your own system manually.
You'll need recent versions of Linux or MacOS, Python3, and possibly a C++ compiler.
Start by cloning this repository and then open a shell:

#+begin_src bash
```bash
python3 -m venv venv
source venv/bin/activate
pip3 install arbor numpy seaborn matplotlib networkx jupyter
jupyter lab
#+end_src
```

While your packages are being installed, you can take a look at the introduction
in ~intro.pdf~. Then, open the ~arbor-tutorial.ipynb~ notebook; everything else
in <intro.pdf>. Then, open the <arbor-tutorial.ipynb> notebook; everything else
should follow from there.

* Useful Links
## Useful Links
- Source code :: https://github.com/arbor-sim/arbor/
- Documentation :: https://docs.arbor-sim.org/en/stable/
- Chat server :: https://app.gitter.im/#/room/#arbor-sim_community:gitter.im
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