Wind the clock back about 50 years, and you would have found the DSKY interface—with a display (DS) and keyboard (KY)—quite familiar. It was frontend to the guidance computer used on the Apollo missions, that ultimately allowed Neil Armstrong to utter that celebrated, “One small step for [a] man, one giant leap for mankind.” The device effectively used a command line.
Continue readingFilm review: Back to the lab
Background:
Interdisciplinary projects are in fashion. Nowadays, most of the top universities in the world offer “interdisciplinary” doctorate programs. It seems that becoming a specialist in a particular field is not enough to progress in science. Now, students must prove their ability to understand and be proficient in different areas. Why study only Chemistry if you can combine it with Statistics, Programming and Biology? The more tools and concepts you can play with the better.
Continue readingJust Call Me EEGor
Recently, I was lucky enough to assist in (who am I kidding…obstruct) a sleep and anaesthesia study aimed at monitoring participants by Electroencephalogram (EEG) in various states of consciousness. The study, run by Dr Katie Warnaby of The Anaesthesia Neuroimaging Research Group at The Nuffield Department of Clinical Neuroscience, makes use of both EEG and functional Magnetic Resonance Imaging (fMRI). The research aim is to learn about the effects anaesthesia has on the brain and and in so doing help us both understand ourselves and understand how to most effectively monitor patients undergoing surgery.
Continue readingWhy you should care about type hints in Python
Duck typing is great. Knowing that as long as my object does what the function expects it to, I can pass it to the function and get my results without having to worry about exactly what else my object might do. Coming from statically-typed languages such as Java and C++, this is incredibly liberating, and makes it easy to rapidly prototype complex and expressive code without worrying about checking types everywhere. This expressiveness, however, comes with a cost: type errors are only caught at runtime, and can be hard to debug if the original author didn’t document what that one variable in that one function signature is expected to look like.
Continue readingConstrained Embedding with RDKit
This blog post explores the RDKit function ConstrainedEmbed.
Continue readingModelling Conformational Flexibility of Kinases in Inactive States
I would like to shamelessly advertise my master thesis project which just got published in Proteins. Keep on reading if you are interested in kinases and/or systematic modelling of protein families.
Continue readingA Brief Introduction to ggpairs
In this blog post I will introduce a fun R plotting function, ggpairs, that’s useful for exploring distributions and correlations.
AIRR community meeting
Hi everyone,
Today is the day for another blog post from me. Last month I attended an AIRR conference in Genoa, Italy (https://www.antibodysociety.org/airrc/meetings/communityiv/). It was the fourth AIRR conference, and I was nice to see lots of field-leading people participating. Compared to the last AIRR meeting almost 2 years ago, the agenda of the conference was dominated by machine learning and big data topics. In my short blog post, I will discuss two talks that covered these two exciting topics.
Continue readingOxford Maths Festival ‘19
The Oxford Maths Festival returned this year and it was tons of fun, at least for this volunteer! I failed to take pictures, but a few opiglets were involved: Flo and company took their VR work for the Ashmolean Dimensions exhibit and demonstrated it at Templars Square, and Conor did a spectacular job pretending to be a police constable for the maths escape room.
Last year Mark blogged about how we demonstrated the German Tank Problem at the festival. I thought this time round I’d share another of the Mathematical Mayhem activities: a game illustrating biased sampling.
Continue readingWhat is the hydrophobic-polar (HP) model?
Proteins are fascinating. They are ubiquitous in living organisms, carrying out all kinds of functions: from structural support to unbelievably powerful catalysis. And yet, despite their ubiquity, we are still bemused by their functioning, not to mention by how they came to be. As computational scientists, our research at OPIG is mostly about modelling proteins in different forms. We are a very heterogeneous group that leverages approaches of diverse scale: from modelling proteins as nodes in a complex interaction network, to full atomistic models that help us understand how they behave.
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