Binder

If you’d like to test out/learn more about how to use Giotto, you can use the Binder Tutorial that we have created. For more information on how this works and what you can do with Giotto, please go to this link.

About Binder

Binder utilizes JupyterHub, repo2docker, and BinderHub to create a docker image built off of a GitHub repository.

Instructions

  1. Simply click this button Binder and a Docker image will be generated.

  2. Wait for your Docker image to be built (if you want to see how this is done, you can click Build logs to display the running script).

  3. Navigate into the Notebooks folder and run whichever notebook you like!

  4. Alternatively, navigate into any of the pre-made scripts for a quick look at how some of these steps come together.

  5. If you run into any errors or have any questions about how the functions and scripts work, feel free to raise an issue with this repository.

  6. If you want to save any of your progress to work on locally, you can download files from the Jupyter notebook directory by clicking the box next to the file name(s) to select it and clicking the Download button on the top left.

Once the image has been created, you will be redirected to a Jupyter notebook landing page. From there, you can navigate into any of the pre-made notebook tutorials and test it out.

Important

  • The first time you build this Binder, it may take while. For some more information on why your session might be taking longer, please refer to this link.

    • Below are some commmon messages that you might see when loading Binder. They are normal! Just give the Binder some more time to load.

Your session is taking longer than usual to start! Check the log messages below to see what is happening.

Launch attempt 1 failed, retrying... Launch attempt 2 failed, retrying...

  • You will have access to 1-2 GB RAM. If you go over 2 GB of RAM the kernel may be restarted.

    • Because we have set up this repo so that you can import pre-processing scripts, you’ll be able to start with any notebook. If your kernel restarts just launch the Binder again!

  • If you are inactive for 10 minutes, the session will shut down. Otherwise, you’ll have up to 6 hours of usage or 1 cpu-hour for more intensive runs.

  • Any changes that you make will not be saved (please do not attempt to push your work back to this repository).

  • Alternatively, if you would like to work on all of this solely locally, you can fork and clone the repository.

About the Tutorial

This binder is modeled after the code tutorials in the HOWTO section of the Giotto website. The goal was to go through the Giotto pipelines with both RNA expression and image (visium) data. This binder should provide a good overview for using Giotto to its fullest potential.

About the Data Used

If you want to do some more exploration with the data we used, you can find more information here:

Be sure to visit the Giotto Tutorial Binder for the Giotto Binder Tutorial for more information.