Why you should care about startups as a researcher
I was recently awarded the EIT Health Translational Fellowship, which aims to fund DPhil projects with the goal of commercializing the research and addressing the funding gap between research and seed...
View ArticleCOSTNET19 Conference
Last month, I attended the COSTNET19 Conference in Bilbao (Spain). This conference is organised by COSTNET, a COST Action which aims to foster international European collaboration on the emerging...
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On The Logic of GOing with Weisfeiler-Lehman
Recently, I was able to attend Martin Grohe’s talk on The Logic of Graph Neural Networks. Professor Grohe of RWTH Aachen University, is a titan of the fields of Logic and Complexity theory. Even so,...
View ArticleThe ultimate modulefile for conda
Environment modules is a great tool for high-performance computing as it is a modular system to quickly and painlessly enable preset configurations of environment variables, for example a user may be...
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Better histograms with Python
Histograms are frequently used to visualize the distribution of a data set or to compare between multiple distributions. Python, via matplotlib.pyplot, contains convenient functions for plotting...
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KAUST Computational Advances in Structural Biology
Last month, I had the privilege of being invited to the KAUST Research Conference on Computational Advances in Structural Biology, held from May 1-3, 2023. This gave me the opportunity to present some...
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Le Tour de Farce 2023
16:30 BST 27/06/2023 Oxford, UK. A large number of scientists were spotting riding bicycles across town, to the consternation of onlookers. The event was the Oxford Protein Informatics Group (OPIG)...
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The workings of Fragmenstein’s RDKit neighbour-aware minimisation
Fragmenstein is a Python module that combine hits or position a derivative following given templates by being very strict in obeying them. This is done by creating a “monster”, a compound that has the...
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Working with PDB Structures in Pandas
Pandas is one of my favourite data analysis tools working in Python! The data frames offer a lot of power and organization to any data analysis task. Here at OPIG we work with a lot of protein...
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Tracking the change in ML performance for popular small molecule benchmarks
The power of machine learning (ML) techniques has captivated the field of small molecule drug discovery. Increasingly, researchers and organisations have employed ML to create more accurate algorithms...
View ArticleQuickly (and lazily) scale your data processing in Python
Do you use pandas for your data processing/wrangling? If you do, and your code involves any data-heavy steps such as data generation, exploding operations, featurization, etc, then it can quickly...
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Exploring multilingual programming
Python is a prominent language in the ML and scientific computing space, and for good reason. Python is easy-to-learn and readable, and it offers a vast selection of libraries such as NumPy for...
View ArticleWhy you should care about startups as a researcher
I was recently awarded the EIT Health Translational Fellowship, which aims to fund DPhil projects with the goal of commercializing the research and addressing the funding gap between research and seed...
View ArticleCOSTNET19 Conference
Last month, I attended the COSTNET19 Conference in Bilbao (Spain). This conference is organised by COSTNET, a COST Action which aims to foster international European collaboration on the emerging...
View ArticleClik here to view.
Pyrosetta for RFdiffusion
I will not lie: I often struggle to find a snippet of code that did something in PyRosetta or I spend hours facing a problem caused by something not working as I expect it to. I recently did a tricky...
View ArticleWhy you should care about startups as a researcher
I was recently awarded the EIT Health Translational Fellowship, which aims to fund DPhil projects with the goal of commercializing the research and addressing the funding gap between research and seed...
View Article