The IMGT have adopted a more permissive licence for their data. That is a really good thing. These days, they also have an API. But the service is somewhat hamstrung by usability issues. Also, detailed and digestible documentation for such a sprawling suite of databases and tools never just appears overnight, so this post includes a demo to help you get started.
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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…
Continue readingInstalling open source PyMOL with pip
TLDR; pip install pymol-open-source
OPIG website and services will undergo routine maintenance on Monday 11 August 2025 at 10:00 UTC
Please note that OPIG’s website and web services will be down for routine maintenance at 10:00 UTC on Monday 11th August 2025 for approximately one hour.
We apologize for any inconvenience this may cause.
Demystifying Git and Merge Conflicts
Git can be an incredibly effective coding tool, but it can also be an incredibly frustrating one. It has a steep learning curve, but you’ll be a lot better off understanding how it works rather than copying and pasting commands from Stack Overflow or ChatGPT. I’ve been there, and things can go very, very wrong.
What is Git?
Git is a version control system which tracks changes in files within a repository. It lets you maintain different versions of that codebase. Not to be confused with GitHub, which is a Git server, or a remote location which serves as the host to codebases in Git. GitHub provides a user-friendly front-end for managing changes and issue tracking. There are plenty of other Git servers, such as Bitbucket and GitLab.
Tips for using Git
Git is massive, and there’s plenty of tutorials and guides out there to help you learn it. This is far from a comprehensive guide, but these are the commands I use on a regular basis. I’ll go over some of the basics, and then some of the niche ones that I’ve found particularly useful.
Continue readingLLM Coding Tools – An Overview
We’ve come a long way since GitHub Copilot first showed us what AI-assisted coding could look like. These days, there’s a whole ecosystem of LLM coding tools out there, each with their own strengths and approaches. In this blog, I’ll give you a quick overview to help you figure out which one might work best for your workflow.
Level 1: Interactive Code Assistance
Continue readingDiagnostics on the Cutting Edge, Software in the Stone Age: A Microbiology Story
The need to treat and control infectious diseases has challenged humanity for millennia, driving a series of remarkable advancements in diagnostic tools and techniques. One of the earliest known legal texts, the Code of Hammurabi, references the visual and tactile diagnosis of leprosy. For centuries, the distinct smell of infected wounds was used to identify gangrene, and in Ancient Greece and Rome, the balance of the four humors (blood, phlegm, black bile, and yellow bile) was a central theory in diagnosing infections.
The invention of the compound microscope in 1590 by Hans and Zacharias Janssen, and its refinements by Robert Hooke and Antonie van Leeuwenhoek, marked a turning point as it enabled the direct observation of microorganisms, thereby linking diseases to their microbial origins. Louis Pasteur’s introduction of liquid media aided Joseph Lister in identifying microbes as the source of surgical infections, whilst Robert Koch’s experiments with Bacillus anthracis firmly established the connection between specific microbes and diseases.
Continue readingDo not forget to add your data folder to .gitignore
It is good practice not to commit a data folder to version control if the data is available elsewhere and you do not want to track changes of the data. But do not forget to also add an entry for this folder to .gitignore because otherwise git iterates over all the files in the folder when checking for file changes, which may take a long time if there are many files.
Making your code pip installable
aka when to use a CutomBuildCommand or a CustomInstallCommand when building python packages with setup.py
Bioinformatics software is complicated, and often a little bit messy. Recently I found myself wading through a python package building quagmire and thought I could share something I learnt about when to use a custom build command and when to use a custom install command. I have also provided some information about how to copy executables to your package installation bin. **ChatGPT wrote the initial skeleton draft of this post, and I have corrected and edited.
Next time you need to create a pip installable package yourself, hopefully this can save you some time!
Continue readingMy 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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