Tag Archives: Software

App-ready databases from Python with SQLModel and FastAPI

Python is ubiquitous for those of us coming into programming from academic research backgrounds, both for generating scientific data and for analysing it. Of course, modern data-driven research only thrives when data is FAIR (findable, accessible, interoperable, and reusable) and traditional relational databases and APIs for interacting with them are a tried-and-true method of ensuring FAIRness. (And in the age of machine learning, the machines need things to be FAIR arguably even more than we do…)

“But I’m a data scientist/computational chemist/bioinformatician!” you protest. “I just (ab)use databases using Python, I don’t make them for someone else to use!” Understandable, but the barrier to entry may be much lower than you think, thanks to two related Python libraries: SQLModel and FastAPI. These powerful tools by developer Sebastián Ramírez (@tiangolo on GitHub) work in concert to make relational databases and APIs much easier to implement for Python natives. Let’s see how they can help…

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On the Joys of vim-like Browsing

Reflections on Pointlessness

One of the great delights in this life is pointless optimisation. Point-ful optimisation has its place of course; it is right and proper and sensible, and, well, useful, and it also does, when first achieved, yield considerable satisfaction. But I have found I soon adjust to the newly more efficient (and equally drab) normality, and so the spell fades quickly.

Not so with pointless optimisation. Pointless optimisation, once attained, is a preternaturally persistent source of joy that keeps on giving indefinitely. Particularly if it involves acquiring a skill of some description; if the task optimised is frequent; and if the time so saved could not possibly compensate for the time and effort sunk into the optimisation process. Words cannot convey the triumph of completing a common task with hard-earned skill and effortless efficiency, knowing full-well it makes no difference whatsoever in the grand scheme of things.

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My take on the Collaborations Workshop (CW) 2024

At the end of April, I attended the CW 2024. This yearly hybrid event organised by the Software Sustainability Institute (SSI) has been running since 2011! The event brings people together to discuss best practices and the future of software in research. This year’s event themes were (1) AI/ML tools for Science, (2) Citizen Science and (3) Environmental sustainability.

As a Research Software Engineer (RSE) working with OPIG, I felt a great curiosity to attend and find out what I could bring of use to the group, as most people work on AI/ML applications. In this blog post, I share a few bits of the event which resonated with me and I found most interesting and relevant to share with my group.

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