Last year, the Structural Antibody Database (SAbDab) listed a record-breaking 894 new antibody structures, driven in no small part by the continued efforts of the researchers to understand SARS-CoV-2.
In this blog post I wanted to highlight the major driving force behind this curve – the huge increase in cryo electron microscopy (cryoEM) data – and the implications of this for the field of structure-based antibody informatics.
Continue readingWhen you wrangle data for a living, you start to wonder why everything takes so darn long. Through five years of introspection, I have come to conclude that two simple factors limit every computational project. One is, of course, your personal productivity. Your time of focused work, minus distractions (and yes, meetings figure here), times your energy and mental acuity. All those things you have little control over, unfortunately. But the second is the productivity of your code and tools. And this, in principle, is a variable that you have full control over.
This is a post about how to increase your productivity, by helping you navigate all those instances when the progress bar does not seem to go fast enough. I want to discuss actionable tools to make your code run faster, and generate more results, with less effort, in less time. Instructions to tinker less and think more, so you can do the science that you truly want to be doing. And, above all, I want to give out advice that is so counter-intuitive that you should absolutely consider following it.
Continue readingIn June, after I finish my PhD, I will be joining Chemify, a new startup based in Glasgow that aims to make chemical synthesis universally accessible, reproducible and fully automated using AI and robotics. After previously talking about “Why you should care about startups as a researcher” and a quick guide on “Commercialising your research: Where to start?” on this blog, I have now joined a science-based startup fresh out of university myself.
Chemify is a spinout from the University of Glasgow originating from the group of Prof. Lee Cronin. The core of the technology is the chemical programming language χDL (pronounced “chi DL”) that, in combination with a natural language processing AI that reads and understands chemical synthesis procedures, can be used to plan and autonomously executed chemical reactions on robotic hardware. The Cronin group has also already build the modular robotic hardware needed to carry out almost any chemical reaction, the “Chemputer”. Due to the flexibility of both the Chemputer and the χDL language, Chemify has already shown that the applications go way beyond simple synthesis and can be applied to drug formulation, the discovery of new materials or the optimisation of reaction conditions.
Armed with this transformational software and hardware, Chemify is now fully operational and is hiring exceptional talent into their labs in Glasgow. I am excited to see how smart, AI-driven automation techniques like Chemify will change how small scale chemical synthesis and chemical discovery more broadly is done in the future. I’m super excited to be part of the journey.
In preparing for battle I have always found that plans are useless, but planning is indispensable.
Dwight D. Eisenhower
Following the previous post about OPIG retreat 2022, and having received numerous requests for recipes, I thought I’d document the process of ensuring that 24 people are kept fed and happy. Recipes at the foot of the post.
Disclaimer – these recipes are entirely my own interpretations, adapted where necessary to suit a range of dietary requirements. They are in no way authentic to any national cuisines and are not intended to be.
Disclaimer II: The Disclaiming – all measurements are approximate. I rarely write down recipes or use precise measurements. Taste as you go, and don’t be afraid to add more salt.
Continue readingComputing is one of the only scientific fields which was once female-dominated. In the 30s and 40s, women made up the bulk of the workforce doing complex, tedious calculations in the fields including ballistics, astrophysics, aeronautics (think Hidden Figures) and code-breaking. Engineers themselves found that the female computers were far more reliable than themselves in doing such calculations [9]. As computing machines became available, there was no precedent set for the gender of a computer operator, and so the women previously doing the computing became the computer operators [10].
However, this was not to last. As computing became commercialised in the 50s, the skill required for computing work was starting to be recognised. As written in [1]:
“Software company System Development Corp. (SDC) contracted psychologists William Cannon and Dallis Perry to create an aptitude assessment for optimal programmers. Cannon and Perry interviewed 1,400 engineers — 1,200 of them men — and developed a “vocational interest scale,” a personality profile to predict the best potential programmers. Unsurprisingly given their male-dominated test group, Cannon and Perry’s assessment disproportionately identified men as the ideal candidates for engineering jobs. In particular, the test tended to eliminate extroverts and people who have empathy for others. Cannon and Perry’s paper concluded that typical programmers “don’t like people,” forming today’s now pervasive stereotype of a nerdy, anti-social coder.”
Continue readingIn our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).
Continue readingThe 2021/2 academic year is now well underway in Oxford, which means a fresh batch of new students getting to grips with some of the bewildering terminology employed here, as well as prospective applicants for next year trying to figure out what on earth a college is and which one they should apply to. As a wizened final year DPhil student I decided to compile an A-Z of Oxford related terms in the hope that someone might find it useful.
Britain’s first public museum, established all the way back in 1678. Home to exhibits covering Ancient Egypt to Modern Art and everything in between.
A termly bill students receive from their college which might cover things like charges for food and accommodation, or fines for not returning books to the library on time.
The 39 colleges are small educational institutions which together comprise the University of Oxford. Every student is a member of a college, each of which has their own set of facilities, including a dining hall, bar, library and student accommodation. Colleges also have their own student unions, called the Junior Common Room (for undergraduates) and Middle Common Room (for postgraduates), which are excellent places to socialise and meet people studying lots of different subjects.
A blog post about ideas.
Ideation is the formation of an idea, but how do we ideate?
The route of the word is “to see”, so when we have an idea we see something. In that moment of realization, we hold on to something quite abstract. Some describe it as a click or pattern or insight. This “seeing” is with the mind, however, not the eyes. Idea also implies sentiment or direction – a path one might say. It’s this last point that resonates with me most. When we are lost, in the sea of thoughts, most of the time the consequences are immediate (no consciousness required). However, sometimes we must pause and ideate. Our path, the next step, is unclear.
Continue readingRecently I have had the opportunity to get a closer look at the submission, review and promotion cycle for a typical academic paper. It was a great learning experience and led to an increase in the number and of research papers, news articles, and reviews I read in preparation. However, on multiple occasions, I did think “I wish I could watch a 2 min video to explain this”. That got me thinking, why couldn’t I and should I be able to?
This is a blog post about using fewer words.
Continue reading