Data Bene

A visit to PGConf.DE 2025 and discussion of PostgreSQL within the context of life sciences

The name of the blog shown with design characteristics like a post-it note

It’s always a pleasure to attend Postgres events, and PGConf.DE 2025 in Berlin was no different. This year’s event reunited old friendships and offered an open and welcoming environment to form new ones. And, of course, it also boasted numerous exciting talks!

At the conference I had the opportunity to present on Postgres within the context of the life sciences (discussed in the next section). And, altogether, I felt this conference had a nice diversity of talks: a selection that spanned Postgres core, its ecosystem, and beyond.

I’m confident that by the end, most if not all attendees left more enriched in some way relative to when they arrived.

Presentations

Leading up to this event I had the honor of one of my talks being accepted. The title was “Postgres and Life Science: From Cells to Stars” and it was organized as a meta-analysis / homage to the extensibility of Postgres and its various applications to the natural world.

In order to best tell this story, I walked the audience through the following five topics of increasing scope:

I enjoyed putting together and presenting the talk, and there was nice discussion afterwards. Two points stood out in particular that I felt would be interesting to address here:

  1. What three technologies (tools / workflows) would benefit most greatly, in terms of increased impact or adoptability, if their complexities were significantly reduced / abstracted away?

  2. During my talk I made a claim that the brain was ACID compliant. While I was referring mostly to the action potentials of neurons, this was rightfully challenged.

1. Identified Tools / Workflows

1. What three technologies (tools / workflows) would benefit most greatly, in terms of increased impact or adoptability, if their complexities were significantly reduced / abstracted away?

1. Image vectorization

Right out of the gate I thought about magnetic resonance scanner image classification. There’s quite a lot of conversation surrounding this topic within the medical community and there are plenty of startups in this space as well. My personal opinion is that there is momentum in the direction of accessibility, but there is still a strong separation between developer and end user. While I don’t know the answer at this point, I would look into pgvector and postgresml as a starting point. Due to this challenge’s involvement of vectors and machine learning, I would consider leveraging an image embedding service to turn the raw MRI output into a format that pgvector might be able to work with.

2. Data management and version control

As a former academic, I can speak to the ubiquitousness of the common spreadsheet (.csv format being less common, but still utilized). What’s more is that files are typically stored in local directories / private server / shared infrastructure, but nevertheless a vanilla folder architecture. One can imagine the potential frictions as the conversation scales to include multiple researchers across multiple groups. Factor in a naturally high student turnover, paired with an “I like doing it my way” mentality, and one could appreciate the value of standards. While improvements could be approached from a number of different angles, I’d like to focus on data management and version control.

Tidy data and good organizational hygiene are hallmarks of success in any field of study. However, tracking changes are most often, if not exclusively limited to text documents. While it might be surprising to the reader, “code repository” is not part of the common academic lexicon. Even the term “Linux” evokes an air of “mysterium tremendum et fascinans” (Otto, 1923). With data security at the top of the mind, self hosted options such as forgejo could potentially benefit life scientists greatly - particularly if there are reservations about storing data online. Instead of having multiple file drafts, e.g., “draft-1_final”, “draft_final_final”, etc, tools such as forgejo can help track progress and give researchers more transparency into past changes (leading into easier cross-team collaboration).

3. Compliance and auditing

Trust is a central topic in any field of research, and in certain circumstances, auditing (or otherwise some form of proof of work) may take center stage. In this case, Postgres and one of its companion extensions, pgaudit, can offer a nice step towards compliance. Due to Postgres’ capabilities, it can sometimes be viewed as intimidating and only suitable for large projects. I think there could be a lot of ubiquity with the publication of a “Postgres for small scale projects” type guide.

Discovery and exposure

At the end of the day, no one will willingly use something unless they know it exists. That’s why discoverability is one of the most fundamental concepts when discussing impact and adoptability. It’s up to the maintainers, contributors, and communities behind these open source tools to share what they’re up to on multiple platforms, as well as different conferences. Honestly, the easiest way to help is to just talk about it and get hands-on.

2. The Brain and ACID Compliance

2. During my talk I made a claim that the brain was ACID compliant. While I was referring mostly to the action potentials of neurons, this was rightfully challenged.

This was another exciting conversation in the post-presentation discussion, and while this really warrants its own blog post, I wanted to quickly share my thoughts. Within one of my slides, I made the claim that the brain is ACID compliant, at least in the sense of transactions being all-or-nothing. Neurons, which are a common cell type in the brain, have a characteristic whereby they receive signals which compile until a threshold is reached and then the neuron sends a signal of its own, or “fires.” This is a gross oversimplification: here’s a quick Wikipedia link for more information.

However, astute audience members righty noted that the brain is complex and has different regions. There is memory loss and there are activities that can alter function and consciousness. However, to what extent do external influences on the brain correspond to a database system? If something corrupts a Postgres database, it is no longer ACID compliant, but it was beforehand. All these points are both valid and interesting. It will be interesting to think on this and write a more formal response.

Concluding Thoughts

To sum things up, this was great conference. I know I speak for all attendees when I extend a thank you to all involved, whether they be staff, volunteers, speakers, or otherwise.

References

Foote, K. J., Grant, J. W. A., & Biron, P. M. (2024). A global dataset of salmonid biomass in streams. Scientific data, 11(1), 1172. https://doi.org/10.1038/s41597-024-04026-0

Giordano, C., & Hadjibagheri, P. (2021, December 11). UK COVID-19 dashboard built using Postgres and Citus for millions of users. Microsoft TechCommunity Blog. https://techcommunity.microsoft.com/t5/azure-database-for-postgresql/uk-covid-19-dashboard-built-using-postgres-and-citus-for/ba-p/3039052

Kazimiers, T., et al. (2021). CATMAID (Collaborative Annotation Toolkit for Massive Amounts of Image Data) [Computer software]. GitHub. https://github.com/catmaid/CATMAID

Krefl, D., & Nienartowicz, K. (2025, January 17). Harnessing Postgres and HPC for petabyte-scale variable star classification in astronomy [Conference presentation]. CERN PGDay 2025, Geneva, Switzerland. https://indico.cern.ch/event/1336647/contributions/5660229/

Otto, R. (1923). The idea of the holy: An inquiry into the non-rational factor in the idea of the divine and its relation to the rational (J. W. Harvey, Trans.). Oxford University Press. (Original work published 1917)

Teixeira, A. de A., & PgHydro Project. (2022). pghydro (Version 6.6) [Computer software]. GitHub. https://github.com/pghydro/pghydro

Wikipedia contributors. (2025, May 16). Action potential. Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Action_potential