From 3840a7ae162f2d521104741e833eb02dbd3ef381 Mon Sep 17 00:00:00 2001 From: Didi Hou Date: Mon, 20 Nov 2023 14:45:26 +0100 Subject: [PATCH 1/5] Update README.md Update the EBRAINS kernel version that should be used to 23.09 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c18ada3..3dcd2a9 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ The Jupyter Notebook `multi-area-model.ipynb` illustrates the simulation workflo 2. On the `Lab Execution Site` page, select a computing center from the given list. 3. If you’re using EBRAINS for the first time, click `Sign in with GenericOAuth2` to sign in on EBRAINS. To do this, you need an EBRAINS account. 4. Once signed in, on the `Server Options` page, choose `Official EBRAINS Docker image 23.06 for Collaboratory.Lab (recommended)`, and click `start`. -5. Once succeeded, you’re now at a Jupyter Notebook named `multi-area-model.ipynb`. Click the field that displays `Python 3 (ipykernel)` in the upper right corner and switch the `kernel` to `EBRAINS-23.02` or `EBRAINS-23.06`. +5. Once succeeded, you’re now at a Jupyter Notebook named `multi-area-model.ipynb`. Click the field that displays `Python 3 (ipykernel)` in the upper right corner and switch the `kernel` to `EBRAINS-23.09`. 6. Congratulations! Now you can run the model. Enjoy!
To run the model, click the `Run` on the title bar and choose `Run All Cells`. It takes several minutes until you get all results.
**Please note**: every time you click the `Try it on EBRAINS` button, the repository is loaded into your home directory on EBRAINS Lab and it overrides your old repository with the same name. Therefore, make sure you follow the [Fork the repository and save your changes](#fork-the-repository-and-save-your-changes) if you make changes and want to save them. @@ -52,7 +52,7 @@ With limited resources, EBRAINS Lab regularly deletes and cleans data loaded on 2. Go to [EBRAINS Lab](https://lab.de.ebrains.eu), log in, and select a computing center from the given list. 3. In the Jupyter Lab, click on the `Git` icon on the left toolbar, click `Clone a Repository` and paste the address of your fork. 4. Now your forked repository of multi-area model is loaded on the server. Enter the folder `multi-area-model` and open the notebook `multi-area-model.ipynb`. -5. Click the field that displays `Python 3 (ipykernel)` in the upper right corner and switch the `kernel` to `EBRAINS-23.02`. +5. Click the field that displays `Python 3 (ipykernel)` in the upper right corner and switch the `kernel` to `EBRAINS-23.09`. 6. Run the notebook! To run the model, click the `Run` on the title bar and choose `Run All Cells`. It takes several minutes until you get all results. 7. You can modify the exposed parameters before running the model. If you want to save the changes you made, press `Control+S` on the keyboard, click the `Git` icon on the most left toolbar, do git commits and push.
To commit, on `Changed` bar, click the `+` icon, fill in a comment in the `Summary (Control+Enter to commit)` at lower left corner and click `COMMIT`.
From ae41ce63bd43dde05fe9be931613630c44a175a3 Mon Sep 17 00:00:00 2001 From: Didi Hou Date: Mon, 20 Nov 2023 14:56:06 +0100 Subject: [PATCH 2/5] Update README.md Enhanced the documentation --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 3dcd2a9..5d6b8a6 100644 --- a/README.md +++ b/README.md @@ -38,7 +38,7 @@ The Jupyter Notebook `multi-area-model.ipynb` illustrates the simulation workflo * If you plan to only run the model, instead of making and saving changes you made, go to [Try it on EBRAINS](#try-it-on-ebrains-1); Should you want to adjust the parameters, save the changes you made, go to [Fork the repository and save your changes](#fork-the-repository-and-save-your-changes). #### Try it on EBRAINS -1. Click [Try it on EBRAINS](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fmulti-area-model&branch=master&urlpath=lab%2Ftree%2Fmulti-area-model%2Fmulti-area-model.ipynb&branch=master). If any error happens during the following process, please close the browser tab and restart the [User instruction](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fmulti-area-model&branch=master&urlpath=lab%2Ftree%2Fmulti-area-model%2Fmulti-area-model.ipynb&branch=master) process again. +1. Click [Try it on EBRAINS](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fmulti-area-model&branch=master&urlpath=lab%2Ftree%2Fmulti-area-model%2Fmulti-area-model.ipynb&branch=master). If any error or unexpected happens during the following process, please close the browser tab and restart the [User instruction](https://lab.ebrains.eu/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FINM-6%2Fmulti-area-model&branch=master&urlpath=lab%2Ftree%2Fmulti-area-model%2Fmulti-area-model.ipynb&branch=master) process again. 2. On the `Lab Execution Site` page, select a computing center from the given list. 3. If you’re using EBRAINS for the first time, click `Sign in with GenericOAuth2` to sign in on EBRAINS. To do this, you need an EBRAINS account. 4. Once signed in, on the `Server Options` page, choose `Official EBRAINS Docker image 23.06 for Collaboratory.Lab (recommended)`, and click `start`. @@ -47,7 +47,7 @@ The Jupyter Notebook `multi-area-model.ipynb` illustrates the simulation workflo **Please note**: every time you click the `Try it on EBRAINS` button, the repository is loaded into your home directory on EBRAINS Lab and it overrides your old repository with the same name. Therefore, make sure you follow the [Fork the repository and save your changes](#fork-the-repository-and-save-your-changes) if you make changes and want to save them. #### Fork the repository and save your changes -With limited resources, EBRAINS Lab regularly deletes and cleans data loaded on the server. This means the repository on the EBRAINS Lab will be deleted automatically after a period of time. To save changes you made, make sure you fork the repository to your own GitHub, then clone it to the EBRAINS Lab, and do git commits and push changes. +With limited resources, EBRAINS Lab regularly deletes and cleans data loaded on the server. This means the repository on the EBRAINS Lab will be periodically deleted automatically. To save changes you made, make sure you fork the repository to your own GitHub, then clone it to the EBRAINS Lab, and do git commits and push changes. 1. Go to our [Multi-area model](https://github.com/INM-6/multi-area-model) under INM-6, create a fork by clicking the `Fork`. In the `Owner` field, choose your username and click `Create fork`. Copy the address of your fork by clicking on `Code`, `HTTPS`, and then the copy icon. 2. Go to [EBRAINS Lab](https://lab.de.ebrains.eu), log in, and select a computing center from the given list. 3. In the Jupyter Lab, click on the `Git` icon on the left toolbar, click `Clone a Repository` and paste the address of your fork. From 765a4a32b12e873d9bd0bd5df8fb907902bcd192 Mon Sep 17 00:00:00 2001 From: Didi Hou Date: Mon, 20 Nov 2023 14:58:17 +0100 Subject: [PATCH 3/5] Update README.md --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index 5d6b8a6..ec5abf4 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,6 @@ A video providing a brief introduction to the model and the code in this reposit Want to start using or simply run the model? Click the button below.
**Please note**: make sure you check and follow our [User instructions](#user-instructions), especially if you plan to make and save the changes, or if you simply need step-by-step instructions.
Try it on EBRAINS - -------------------------------------------------------------------------------- ### User instructions From ad4825bac465ef5c39917c044dd6fd2fbe5b0c92 Mon Sep 17 00:00:00 2001 From: Didi Hou Date: Mon, 20 Nov 2023 14:58:50 +0100 Subject: [PATCH 4/5] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index ec5abf4..5d6b8a6 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,7 @@ A video providing a brief introduction to the model and the code in this reposit Want to start using or simply run the model? Click the button below.
**Please note**: make sure you check and follow our [User instructions](#user-instructions), especially if you plan to make and save the changes, or if you simply need step-by-step instructions.
Try it on EBRAINS + -------------------------------------------------------------------------------- ### User instructions From 8e3f2c8a634c881dcfba783efd24cbb986378dff Mon Sep 17 00:00:00 2001 From: Didi Hou Date: Mon, 20 Nov 2023 15:55:29 +0100 Subject: [PATCH 5/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5d6b8a6..9528759 100644 --- a/README.md +++ b/README.md @@ -47,7 +47,7 @@ The Jupyter Notebook `multi-area-model.ipynb` illustrates the simulation workflo **Please note**: every time you click the `Try it on EBRAINS` button, the repository is loaded into your home directory on EBRAINS Lab and it overrides your old repository with the same name. Therefore, make sure you follow the [Fork the repository and save your changes](#fork-the-repository-and-save-your-changes) if you make changes and want to save them. #### Fork the repository and save your changes -With limited resources, EBRAINS Lab regularly deletes and cleans data loaded on the server. This means the repository on the EBRAINS Lab will be periodically deleted automatically. To save changes you made, make sure you fork the repository to your own GitHub, then clone it to the EBRAINS Lab, and do git commits and push changes. +With limited resources, EBRAINS Lab regularly deletes and cleans data loaded on the server. This means the repository on the EBRAINS Lab will be periodically deleted. To save changes you made, make sure you fork the repository to your own GitHub, then clone it to the EBRAINS Lab, and do git commits and push changes. 1. Go to our [Multi-area model](https://github.com/INM-6/multi-area-model) under INM-6, create a fork by clicking the `Fork`. In the `Owner` field, choose your username and click `Create fork`. Copy the address of your fork by clicking on `Code`, `HTTPS`, and then the copy icon. 2. Go to [EBRAINS Lab](https://lab.de.ebrains.eu), log in, and select a computing center from the given list. 3. In the Jupyter Lab, click on the `Git` icon on the left toolbar, click `Clone a Repository` and paste the address of your fork.