As someone who works with T cell antigen receptor (TCR) and peptide-major histocompatibility complex (pMHC) data, I have found several Python packages to be very useful for eliminating tedious steps in data cleaning and feature engineering stages.
Continue readingMonthly Archives: February 2026
Building a “Second Brain” – A Functional Knowledge Stack with Obsidian
Whilst I always enjoy the acquisition of knowledge, I’ve always struggled with depositing it usefully. From pen and paper notes with a 20 colour theme which lost value with each additional colour, to OneNote or iPad GoodNotes based emulations of pen and paper, it’s been a constant quest for the optimal note taking schema. Personally there are 3 key objectives I need my note taking to achieve:
- It must be digitally compatible and accessible from any device.
- It must comfortably handle math and images.
- It must be something I look forward to – the software needs to be aesthetically clean, lightweight with none of the chunkiness of Microsoft apps, and highly customisable.
For me the solution to this was Obsidian, the perhaps more cultified sibling to Notion. Obsidian is a note taking application that uses markdown with a surprising amount flexibility, including the ability to partner it with an LLM which I’ll explore in this blog, alongside my vault organisation do or dies, and favourite customisations.
Continue readingNew DPhil/PhD Programme in Pharmaceutical Science Joint with GSK!
Many OPIGlets found their way into a DPhil in Protein Informatics through our Systems Approaches to Biomedical Sciences Industrial Doctoral Landscape Award, which was open to applicants 2009-2024. This innovative course, based at the MPLS Doctoral Training Centre (DTC), offered six months of intensive taught modules prior to starting PhD-level research, allowing students to upskill across a diverse range of subjects (coding, mathematics, structural biology, etc.) and to go on to do research in areas significantly distinct from their formal Undergraduate training. All projects also benefited from direct co-supervision from researchers working in the Pharmaceutical industry, ensuring DPhil projects in areas with drug discovery translation potential. Regrettably, having twice successfully applied for renewal of funding, we were unsuccessful in our bid to refund SABS in 2024.
Happily though, we can now formally announce that our bid for a direct successor to SABS, the Transformative Technologies in Pharmaceutical Sciences IDLA, has been backed by the BBSRC, and we will shortly be opening for applications for entry this October [2026]. As someone who benefited from the interdisciplinary training and industry-adjacency of SABS, I’m thrilled to be a co-director of this new Programme and to help deliver this course to a new generation of talented students.
Creating scientific figures in Inkscape
As a rule in scientific education, at some point between starting undergraduate and doing professional research it would seem we are expected to simply start knowing how to do things, without necessarily any formal training. One example in my degree was writing code, but another, as it turns out, is drawing figures for papers. Today, I would like to assist with the latter!
Inkscape https://inkscape.org/ is free and very powerful. Paired with python plotting and the textext plugin https://github.com/textext/textext it can really handle a lot, from abstract concepts to technical diagrams to artistic illustrations. Here I’ll just describe the workflow for including LaTeX and plots generated in Matplotlib, the rest (the artsy bit) is more about playing around with the different tools to find an ideal workflow.
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