HuBMAP Workspaces Hackathon a Success!
HuBMAP Workspaces Hackathon a Success!
October 23, 2024
Workspaces details example, showing a group of datasets and attached templates.
The HuBMAP Data Portal (Harvard) and HuBMAP Consortium (PSC) HIVE teams held a HuBMAP Workspaces Hackathon September 20 - Oct 4. Over 30 individuals across ten teams participated in the event including Consortium members and participants from outside the consortium. The first and last days of the Hackathon included live events over Zoom where participants learned about Workspaces and the Data Portal, worked cooperatively, shared about their experiences and results, and competed for prizes. During the two intervening weeks, teams and individuals worked asynchronously on a variety of Workspace-based projects, using and creating Workspace templates to analyze HuBMAP and their own data. The event introduced participants to Workspaces as well as HuBMAP data and tools. The Hackathon organizers gained valuable feedback from participants about how to improve Workspaces and make HuBMAP resources easier to access.
Workspaces is a joint effort by the Harvard and PSC HIVE Teams. The Harvard team contributes user interfaces, portal integration, and workspace templates, while the PSC team focuses on the computational infrastructure. The target audience for Workspaces includes computational analysts in HuBMAP and elsewhere as well as students and trainees learning about spatial and single-cell data analysis approaches. Workspaces supports analysis of HuBMAP and user-provided data directly in the data portal without the need to download HuBMAP data. You can also upload your own data (currently size-limited). Compute resources for Workspaces provided by PSC on hardware funded by HuBMAP. Workspaces uses the popular JupyterLab environment and supports Python and R. Analysis templates demonstrate workspace capabilities and facilitate quick startup for common analyses.
Three of the ten teams who participated, iST, SHlee, and JEFWork, received awards of $400 from Harvard University. Members of the NIH HuBMAP Working Group reviewed the teams’ findings and announced the award winners following group presentations on October 4th. Based on the event's outcomes, the organizers hope to hold similar events in the future, with even greater participation from outside of the HuBMAP Consortium.
Example of a CODEX static visualization plot in Workspaces’ Jupyter Lab environment.
Note: Thanks to Tiffany Liaw of the Harvard Team for providing Workspaces and Jupyter Lab illustrations.