Packaging Jupyter notebooks as installable desktop apps using LabConstrictor
This tool solves deployment and usability problems for academic developers and researchers in life sciences, though it is incremental as it builds on existing CI/CD and packaging methods.
The paper tackles the problem of underused open-source academic software in life sciences by addressing practical barriers like installation and reproducibility issues with Jupyter notebooks, resulting in LabConstrictor, a tool that packages notebooks into one-click installable desktop apps to simplify distribution and sharing.
Life sciences research depends heavily on open-source academic software, yet many tools remain underused due to practical barriers. These include installation requirements that hinder adoption and limited developer resources for software distribution and long-term maintenance. Jupyter notebooks are popular because they combine code, documentation, and results into a single executable document, enabling quick method development. However, notebooks are often fragile due to reproducibility issues in coding environments, and sharing them, especially for local execution, does not ensure others can run them successfully. LabConstrictor closes this deployment gap by bringing CI/CD-style automation to academic developers without needing DevOps expertise. Its GitHub-based pipeline checks environments and packages notebooks into one-click installable desktop applications. After installation, users access a unified start page with documentation, links to the packaged notebooks, and version checks. Code cells can be hidden by default, and run-cell controls combined with widgets provide an app-like experience. By simplifying the distribution, installation, and sharing of open-source software, LabConstrictor allows faster access to new computational methods and promotes routine reuse across labs.