Using GitPod to explore the .ipynb tutorials

[Krista Pipho]

When I use the GitPod version of the .ipynb files to explore the tutorials, visualizations do not load. Do you have any recommendations for remedying this? 

Is there any other 'getting started' materials useful to a new user not familiar with C programming? 

Best, 

Krista 

[Umar Faruk]

Hi Krista, I apologize for the delay in responding to your message. Thank you for your interest in BioDynaMo. Regarding the Jupyter visualization issues you've mentioned, we are aware of this issue but atm cannot provide support for it. Instead, to fully leverage BioDynaMo, we recommend proceeding with a local installation. You can find the necessary documentation for installing BioDynaMo on a Linux or MacOS machine at the following link: Should you encounter any issues during the installation process, please don't hesitate to reach out to us either on our forum or via our Discord server: As for your query about learning C++ programming as a beginner, I understand that you're seeking materials suitable for a new user unfamiliar with C programming. Although we don't currently have resources specifically dedicated to this, we do have a 'Getting Started' guide and a walkthrough of the "Tumour Concept" demo which might prove useful. You can find these here: Additionally, learning C++ can a useful tool. If you're open to it, we recommend the following resources. These, along with the examples on our GitHub, should help you establish a basic understanding of BioDynaMo and C++ programming:

Best,

Umar A

[Cayla Harris]

Hi Krista,
As Umar has mentioned there are some great resources for getting started with the BioDynaMo simulations, of which he has linked. Please feel free to get in touch directly with me at www.linkedin.com/in/caylaharris-45a436184, as I have been working with BioDynaMo a lot recently as someone coming from a background in biochemistry/genetics rather than programming, so I may have already encountered other issues you may have in the future!

Best,
Cayla Harris

[Tobias Duswald]

Dear Krista,

I just tried to reproduce your problem, but I cannot. The visualizations work perfectly fine if I open a notebook (I tried ST01) via GitPod (see screenshot).

Since GitPod uses a container, the backend must behave identically for you. You could try a different browser (even though it should not make any difference).

To get to the screenshot above, I did the following.

1. open https://biodynamo.org/examples/notebooks in the browser (Safari in my case)

2. Go to ST01 (Create agents in 3D space) and click the green "Try now" button

3. Log in with method of choice (GitHub for me)

4. On the page "new workspace" click continue.

5. Now the gitpod thing loads (might take a while)

6. VS code interface opens and asks if it can open a new window (this might depend on the browser; maybe your browser blocks that; also, if you take a long time, this message may somehow disappear. Like when I took the screenshot and come back it was gone.) Anyhow, here you have to click "open". This will open the notebook in a new tab or window (window for me)

7. Now, simply execute one cell after another. (I click the cell and press "shift + return" on macOS; you may also click play on the top header. Execute all cells in order). Everything works perfectly fine for me. Note that you can click the images, zoom, and rotate.

I hope that helps. If you get stuck along the way, please let me know where you get stuck. If possible, please also indicate as much information as possible (browser, operating system, screenshots ...) such that we can see if we can reproduce the issue.

Best, Tobias