Episode 287: Alan Rubin on MaveDB

Guest Alan Rubin Panelist Richard Littauer Show Notes On this episode of Sustain, Richard Littauer sits down with computational biologist Alan Rubin to explore how open source software supports scientific research, clinical genetics, and cancer-related data infrastructure. Their conversation centers on MaveDB, a project that began as a way to organize hard-to-find variant data from research papers and has since evolved into a valuable resource for both scientists and clinicians. Along the way, they discuss infrastructure funding, research software sustainability, and why open source communities and academic researchers have a lot to learn from each other. Press download now to hear more! [00:01:24] Alan explains his role leading a research group focused on genomics, cancer medicine, and improving patient care through genetics. [00:02:46] We learn more about what MaveDB does. [00:06:52] Alan details why a database was needed. [00:08:26] Alan shares how the project grew out of collaboration, PyCon AU inspiration, Django, and Python tooling that let a small team build a practical research database. [00:11:54] There’s a discussion on the infrastructure funding problem and Alan explains a major theme is how hard it is to fund scientific infrastructure, since most grants favor new discoveries rather than maintaining shared tools and databases. [00:17:55] The project took a major turn when clinical geneticists began using the data to interpret patient variants, pushing the team to rethink the interface and user needs. [00:21:13] Alan describes the new clinical-facing interface, Mave for Medicine (MaveMD), designed to help doctors evaluate specific variants for diagnosis and treatment decisions. [00:22:02] Alan talks about managing the project through a distributed team, shared responsibilities, and a role that now centers more on direction, priorities, and community than day-to-day coding. [00:23:36] They discuss why research software rarely attracts hobbyist contributors, even when the mission is compelling, and how scientific projects often function more like small product teams. [00:27:44] Alan makes the case that scientists often learn more about improving their software craft at events like PyCon than at discipline-specific conferences. [00:30:38] Alan highlights how academic software depends heavily on mature, well-documented open source tools and encourages more connection between technical communities and scientific work. [00:34:15] Find out where you can learn more about MaveDB and Alan’s work. Quotes [00:10:04] “We quite literally followed the Django Girls tutorial, but instead of a building a blog, we built a database for research scientists.” [00:12:35] “Infrastructure is something everybody wants to have it exist and nobody wants to pay for.” [00:26:08] “I have never been successful in engaging the broader open source community, despite having tried many times to contribute to this or any other scientific project.” [00:31:01] “I think people who work in OSS should be excited about the kind of stuff that their work is enabling, even if they don’t really hear about it.” Spotlight [00:35:44] Richard’s spotlight is the book, News of the Dead. [00:36:22] Alan’s spotlight is The Global Alliance for Genomics & Health (GA4GH) and all the good work they’re doing. Links SustainOSS [email protected] [email protected] SustainOSS Discourse SustainOSS Mastodon SustainOSS Bluesky SustainOSS LinkedIn Open Collective-SustainOSS (Contribute) Richard Littauer Socials Alan Rubin LinkedIn Dr. Alan Rubin Website (The University of Melbourne) PyCon AU 2026, Brisbane, August 26-30 Sustain Podcast- Episode 286: Jack Skinner of PyCon AU and Regional Confs Sustain Podcast- Episode 176: Maintainer Month with Russell Keith-Magee & Uriel Ofir Django Girls PyCon AU 2023-“Building a biological database with Python”- Alan Rubin (YouTube) Sustain Podcast- Episode 135: Tracy Hinds on Node.js’s CommComm and PMs in Open Source Sustain Podcast-Episode 190: Karen Sandler on Software Freedom Conservancy (SFC) Original database paper (Pub Med) Database update paper (Pub Med) Preprint on the clinician-oriented interface Variant scoring tools for deep mutational scanning (Pub Med) Atlas of Variant Effects MaveDB News of the Dead Global Alliance for Geonomics & Health (GA4GH) Sponsor CURIOSS Credits Produced by Richard Littauer Edited by Paul M. Bahr at Peachtree Sound Show notes by DeAnn Bahr Peachtree Sound Special Guest: Alan Rubin.