Software

I maintain or have contributed to the following pieces of open source software. For a list of additional projects for which I have contributed, please see my GitHub profile.

GenePattern Notebook is an extension for Jupyter Notebook which bridges the functionality of Jupyter and GenePattern. It provides access to hundreds of bioinformatic tools in Jupyter Notebook, all with a friendly user interface.

Notebook Repository is a web service intended to run alongside a JupyterHub instance. It integrates with the JupyterHub authenticator API, providing notebook publication and sharing functionality within the proxied Jupyter Notebook instances.

GenePattern Server is a platform for bioinformatic research that wraps hundreds of analytic tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry and network analysis. It also provides a REST API and queueing system integrations.

GenePattern Python Library is a Python wrapper for the GenePattern API. It provides programmatic access for searching and selecting analyses, uploading files, submitting jobs, retrieving the analysis results and sending those results to a downstream step in an analysis pipeline.

Jupyter WYSIWYG Editor is an extension for Jupyter Notebook that adds WYSIWYG editing functionality to markdown/HTML cells. It does this by integrating the popular CKEditor.

GenomeSpace is a cloud-based interoperability framework, bridging the gaps between a diverse set of popular bioinformatic tools. This makes it possible to frictionlessly use the available analyses and visualizations in each tool with others in the GenomeSpace ecosystem.

IGV.js Jupyter is a Python wrapper and nbextension for the JavaScript version of Integrative Genomics Viewer (IGV.js), allowing the popular genomic visualization tool to be easily configured and embedded inside the Jupyter Notebook environment.

Django Simple Ticket is a simple ticket-tracking app that can easily be dropped into a new or existing Django site. It aims for bare bones simplicity rather than elaborate features, minimizing dependencies and allowing the app to be set up in as little time as possible.