Identifying malaria phenotype papers with GPT-3

Visit Some years ago I launched PhenoPlasm which aims to catalogue all reported phenotypes in Plasmodium in a systematic machine- (and human-) readable format. At the time I tried to populate it with all reported phenotypes in Plasmodium falciparum to date, using a series of searches on Google scholar.


Python package / CLI tool for easy alignment of viral sequences to reference (using minimap2 under the hood)

Investigating the latest round of REACT

The latest round of the REACT study has come out, and been quite controversial. Let’s examine some of the raw data behind it. library(tidyverse) Let’s download the REACT data and process it into a nice format:


A tool for exploring spatiotemporal changes in lineages


A small tool to look up nucleotides from codon positions for SARS-CoV-2 and vice-versa


The library used to select SARS-CoV-2 samples for sequencing in the United Kingdom