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Notebooks FAQ

This article answers common questions about the LifeOmic Platform Notebook feature. For more documentation, see My Notebooks.

What are LifeOmic Notebooks?

LifeOmic Notebooks are a fully managed Jupyter Notebook service that provides every clinical researcher, bioinformatician, and data scientist the ability to analyze large and small clinical data sets with ease.

Why Jupyter for Notebooks?

The choice of JupyterHub provides an open-source ecosystem for writing and executing code in a reproducible and shareable manner.

What language runtimes are available?

R, Python, and Julia are available by default. Other language runtimes may be installed when necessary by opening up a notebook live terminal.

How long does my Notebook session last?

24 hours

What access control does LifeOmic Notebooks enforce?

LifeOmic Notebooks adhere to LifeOmic Platform's Access Control system (Groups + ABAC Policies).

What services can LifeOmic Notebooks access on the LifeOmic Platform?

The list of available services are part of the LifeOmic Platform SDK for Python.

What connectivity is available to a LifeOmic Notebook?

An internet connection is available. You can use it to bring in data from external sources like from a public repository. Examples are: ClinVar, OncoKB

Available egress ports:

  • DNS: 53
  • HTTP: 80
  • HTTPS: 443
  • SSH: 22

What can be customized with my own tool packages across Notebook instances?

In a Notebook terminal, adding a bin directory in your $HOME directory of your notebook instance is where the binaries can be added and then made available by adjusting your PATH variable in your .profile.

How does LifeOmic Notebooks secure my notebook data and filesystem?

Data in LifeOmic Notebooks is encrypted at rest and in transit to and from the LifeOmic Platform.

How do I securely share notebook file (.ipynb) with PHI output?

Upload the notebook file .ipynb to a LifeOmic Platform project that has project collaborators. Users that have access to this project can see it and download it to their notebook instance.

Use the LifeOmic Platform SDK for Python or the CLI (lo files-upload --help) to upload the notebook file.

How do I share notebook code?

LifeOmic Notebooks can interact with public and private source code repositories like git.

PHI NOTE: Notebook output can contain PHI data. You can clear execution outputs from a notebook before storing it in source control.

PHI NOTE: For those Notebooks which have PHI output and sharing, store and share those notebooks to a LifeOmic Platform project.

What compute resources are available for a Data Science Notebook?

The guaranteed resources for a Data Science notebook are the following:

  • CPU: 3
  • Memory: 12 GB

What Data Science tools are available by default?

Tools like tidyverse (R) and pandas (Python) are available. For more information, see Notebook Runtime Environment.

What compute resources are available for a Deep Learning Notebook?

The guaranteed resources for a Deep Learning notebook are the following:

  • CPU: 8
  • Memory: 56 GB

What Deep Learning and Machine Learning tools are available by default?

CUDA Toolkit, TensorFlow (and TensorBoard), PyTorch, and MXNet. For more information, see Notebook Runtime Environment.