Back in 2021, I highlighted the annual fragment-to-lead (F2L) success stories from 2019 [Blog post] [Paper]. This is one of my favourite annual publications, and I’m delighted to see that it’s still going strong. In this post, I’ll discuss the 2023 edition that was published in at the start of 2025 [Paper].
Scientists pride themselves on clear, logical and concise communication. So naturally, the process for publishing our research involves an absurd number of formalities, like coming up with 700 slightly different ways to ‘thank the reviewer for their insightful comment’. Nevertheless, I’m told this is all a necessary part of spreading your beautiful researcher butterfly wings—and frankly, I’m enough years into my DPhil to stop questioning every quirk of academia. However, the current protocol for new researchers wanting to learn the moves to this bizarre dance seems to be begging postdocs/ old timers for examples of cover letters, marked-up manuscripts, and reviewer responses. To attempt to save everyone some time, I thought I’d provide some guidance and templates here.
Continue readingA common scenario we come across is that we have a main manuscript document and a supplementary information document, each of which have their own sections, tables and figures. The question then becomes – how do we effectively cross-reference between the documents without having to tediously count all the numbers ourselves every time we make a change and recompile the documents?
The answer: cross referencing!
Continue readingAs a first year PhD student, it is not an uncommon thing to be asked to write a review paper on your subject area. It is both a great way to get acquainted with your research field and to get the background portion of your thesis completed early. However, it can seem like a daunting task to go from knowing almost nothing about your research field to producing something of interest for experts who have spent years studying your subject matter.
In my first year, I was exactly in this position and I found very little online to help guide this process. Thus, here is my reflective look at writing a review paper that will hopefully help someone else in the future.
Continue readingYou might have created the most esthetic figures for your last presentation with a beautiful colour scheme, but have you considered how these might look to someone with colourblindness? Around 5% of the gerneral population suffer from some kind of color vision deficiency, so making your figures more accessible is actually quite important! There are a range of online tools that can help you create figures that look great to everyone.
Continue readingIn an attempt to ease the transition from Word to LaTeX for some of my colleagues (*cough* Alex *cough*) this blog post covers some LaTeX tricks I use most frequently when preparing manuscripts. It’s pitched at someone who is already familiar with the basic syntax of paragraphs, figures and tables.
Continue readingAnalysing, comparing and communicating the predictive performance of machine learning models is a crucial component of any empirical research effort. Pandas, a staple in the Python data analysis stack, not only helps with the data wrangling itself, but also provides efficient solutions for data presentation. Two of its lesser-known yet incredibly useful features are df.to_markdown() and df.to_latex(), which allow for a seamless transition from DataFrames to publication-ready tables. Here’s how you can use them!
We’ve been investigating deep learning-based protein-ligand docking methods which often claim to be able to generate ligand binding modes within 2Å RMSD of the experimental one. We found, however, this simple criterion can conceal a multitude of chemical and structural sins…
DeepDock attempted to generate the ligand binding mode from PDB ID 1t9b
(light blue carbons, left), but gave pretzeled rings instead (white carbons, right).
OPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).
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If you are like me, you can happily write code for hours and hours on end but as soon as you need to write a paper you end up staring at a blank page. Luckily, I have come up with a fool proof way to trick myself into thinking I am coding when in reality I am finalling getting around to writing up the work my supervisor has been wanting for the last month. Introducing Latex and git- this was my approach to draft a review paper recently and in this blopig post I will go through some of the ups and downs I had using these tools.
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