Subtitle: a series of sickening facts I’m interested in the role of the gut microbiome in infection, especially in countries with a high burden of infectious diseases such as Malawi. Therefore, I did a literature search on PubMed for papers on the microbiome from these kinds of country (full text of the search here). The…

I’m having a play around with some AI tools for literature searching and I came across the autoresearcher tool (link). Here is a comparison of the output of autoresearcher with ChatGPT4. TL;DR The question I asked both tools – “what is the role of the microbiome in mediating salmonella exposure outcomes?” autoresearcher output “The microbiome…

I was interested in getting a list of countries with a “high burden of infectious diseases”. From googling around, I found this nice image from Our World in Data (I love them! Source, with CSV etc). The underlying data from this comes from the Global Burden of Disease (GBD) initiative at the Institute of Health…

For some unfathomable reason some journals (e.g. Lancet journals) require you to use floating decimal places instead of normal ones. This is a real pain to do, because you can’t just do a find and replace because that would also replace the full stops. This is an opportunity to use a regex! ChatGPT tells us…

There have been some recent changes to the conda/mamba ecosystem, see obligatory xkcd. This is my current way of creating a fresh install of conda. Setting libmamba as the conda solver should allow you mamba-like speed, while at the same time letting you just install programs like `conda install`.