On June 15, 2026, the main, freely available GenePattern server, cloud.genepattern.org, will be retired from service and all user data deleted. If you have any data you would like to retain, please download it before that date. This notice also applies to the GenePattern Notebook and g2nb.

If you would like to use any of the GenePattern analyses or run GenePattern locally, you can do any of the following:

Run a local GenePattern server. Instructions can be found on the releases page at https://github.com/genepattern/genepattern-server/releases
Run GenePattern modules via an LLM. Use the local GenePattern runner utility https://github.com/genepattern/local_genepattern_runner_mcp to run analyses on your own computer without a GenePattern serve>
Download the GenePattern modules and run them as command-line tools. The collection of publicly released GenePattern modules is available at https://github.com/genepattern/GenePatternModuleCatalog/.

The GenePattern website, www.genepattern.org, will continue to be available.

It has been the pleasure of the GenePattern team to serve the analysis needs of the worldwide genomics community since 2004.

GenePattern Notebook

Integrating genomic analyses with interactive notebooks

Check out our Notebook Library

Get started with our Tutorial Notebook

Try our beta of GenePattern Notebook on JuypterLab

Use GenePattern Notebook

Bioinformatics Analysis

Hundreds of genomic analysis tools available from within a notebook, no programming required

Notebook Environment

Executable notebooks based on and compatible with Jupyter Notebooks, accessible through a browser, no installation required

Notebook Library

Browse a collection of genomic and machine learning notebooks and adapt them for your own use

Publish and Share

Share a notebook with a collaborator or publish it in our library

Notebook Projects

Develop notebooks within separate customizable environments

Publications

Ensure reproducibility of your methods by adding a link to your notebook in a publication

JupyterLab (beta)

Try our beta version of GenePattern Notebook on JupyterLab

External Resources

Easy access to web-based genomic resources from within a notebook

For Developers

pip install genepattern-notebook
conda install -c genepattern genepattern-notebook

Also available in Docker
Fork us on Github

How to Cite

Reich et al. The GenePattern Notebook Environment. Cell Systems. 2017(5):149-51

In the Press

	"GenePattern Notebook is a great tool for researchers with large molecular datasets and makes it easy to get started on your data analysis"
	"Informatics Technology for Cancer Research Program Drives and Fosters Community of Cancer Informatics Researchers: An *AMARETTO Tool Success Story"
	"GenePattern Notebook for analysis and exploration of single-cell transcriptomic data"
	"GenePattern Notebook: Integration of Electronic Notebooks with Bioinformatics Tools for Genomic Data Analysis"
	"TechBlog: Jupyter powers bioinformatics, again"
	"GenePattern Notebook Environment Needs Only A Web Browser To Run Analyses"
	"Broad's GenePattern Now Has 'Notebook' Aggregation, Collaboration Features"

GenePattern Notebook is developed in the lab of Jill Mesirov at University of California, San Diego

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