IDR and Analysis

We have a set of notebooks and apps that can be run in several environments managed by third party. IDR mainly uses BinderHub. The notebooks can be run by anyone without a login. They are available to anyone interested in exploring and mining the diverse and vast range of image data and metadata in the IDR. All notebook sessions are subject to available resources, are limited by the network resources they can access, and will automatically terminate after a period of inactivity. You should consider the notebook environments as suitable for temporary storage only. Below is a list of environments currently supported.

• The public BinderHub mybinder.org
• A dedicated BinderHub binder.bioimagearchive.org hosted EMBL-EBI
• Some notebooks can be run in Google Colab

If you are interested in developing your own data analysis notebooks on our analysis platform please contact us with your GitHub username. This will give you more computational resources including scratch storage space than is available through the public access.

We will do our best to maintain this scratch space across upgrades, though in the event of unforeseen issues we may need to delete all scratch space, and you should consider it as suitable for temporary storage only. Your scratch space may be deleted without warning if you have not logged in for over a month.