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LifeOmic Notebooks FAQ

General

What are LifeOmic Notebooks?

LifeOmic Notebooks are a fully managed Jupyter Notebook service that provides every clincial 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 sharable 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 the PHC's Access Control system (Groups + ABAC Policies).

What services can LifeOmic Notebooks access on the PHC?

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

What connectivity is available to a LifeOmic Notebook?

An internet connection is available for one to bring in data from external sources like from 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?

LifeOmic Notebooks store data encrypted at rest and in transit to and from the PHC.

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

One will have to upload the notebook file .ipynb to a PHC project that has project collaborators so that others who have access to this project can see it and download it to their notebook instance.

This can be done using the PHC SDK for Python or the CLI (lo files-upload --help).

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. One can clear execution outputs from a notebook before storing in source control.

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

Data Science

What compute resources are available for a Data Science Notebook?

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

  • CPU: 3
  • Memory: 12 GB

What Data Science tools are available by default?

Tools like tidyverse (R) and pandas (Python) are available. More details can be reviewed on the LifeOmic Notebook User-Guide.

Deep Learning

What compute resources are available for a Deep Learning Notebook?

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

  • CPU: 8
  • Memory: 56 GB
  • GPU: 1 NVIDIA GPU

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

CUDA Toolkit, TensorFlow (and TensorBoard), PyTorch, and MXNet. More details can be reviewed on the LifeOmic Notebook User-Guide.


Last update: April 22, 2020