All Categories - John Lees' blog

All Categories

bioinformatics

Mini-review of 'Compressive Pangenomics Using Mutation-Annotated Networks' (PanMAN)

RapidNJ for M1 macs

Using the new Microreact API

Porting a bioinformatics tool to the web using WebAssembly, React and javascript

Thoughts on 'Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species'

reviews

Mini-review of 'Compressive Pangenomics Using Mutation-Annotated Networks' (PanMAN)

Video games in 2023 -- five good ones

Mercury Prize 2023

Annual conference, Microbiology Society (2023, Birmingham)

Favourite video games 2022

statistics

Model flexibility and number of parameters

Did 1.27M people die from AMR in 2019?

When to use log scales

p-value < 2.2e-16

Plots that went wrong

linux

RapidNJ for M1 macs

Creating a conda package with compilation and dependencies

conda build: libarchive: cannot open shared object file: No such file or directory

Installing phyx without sudo

Sorting a massive file

science

Powerpoint, Biorender and AI

One hundred days and one hundred lines of code

Host/pathogen data for 'Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis' available on EGA

Model flexibility and number of parameters

Quantify everything, all of the time

programming

Rust take two -- I guess I'm a rust guy now?

Learning rust as a C++/python programmer (advent of code 2021)

Easy debugging of C/C++/CUDA python extensions

Porting a bioinformatics tool to the web using WebAssembly, React and javascript

Things I have learnt about porting algorithms to GPUs (using CUDA)

python

mamba saved my CI

Easy debugging of C/C++/CUDA python extensions

Plots that went wrong

Readthedocs failing to build: module 'setuptools.build_meta' has no attribute '__legacy__'

Paper summary – PopPUNK for bacterial epidemiology

fedora

Samsung Galaxy S3 with Fedora

Installing Times New Roman in fedora

How to automatically start tinc on Fedora 17

How to install texlive (full) on Fedora 17 - and why

How to set up SSH certificates on a Fedora 17 client

latex

A latex bibliography style I like (Nature style in biblatex)

DPPC (Dipalmitoylphosphatidylcholine) DSPC and DMPC in Latex

Using custom text when using ref in latex

How to install texlive (full) on Fedora 17 - and why

os-x

Removing helperamc (Advanced Mac Cleaner) OS X

R packages break after OS X upgrade

Threads, vectors and references in C++11 on OS X

Upgrade OS X 10.8 -> 10.10 (Yosemite) breaks perl, homebrew, gvim

pneumococcus

Host/pathogen data for 'Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis' available on EGA

Paper summary – Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

Conservation of core genes in S. pneumoniae

Expression modules in S. pneumoniae

paper-summary

Thoughts on 'Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species'

Paper summary – Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

Paper summary – PopPUNK for bacterial epidemiology

physics

Sum from i=1 to N of ik^i (for Helix-Coil zipper model)

DPPC (Dipalmitoylphosphatidylcholine) DSPC and DMPC in Latex

Converting .ndv files into .csv (for the UV/Vis nanodrop spectrometers)

scripts

Firth regression in python

Running bugwas + gen files

Converting .ndv files into .csv (for the UV/Vis nanodrop spectrometers)

conferences

Annual conference, Microbiology Society (2023, Birmingham)

Annual conference, Microbiology Society (2022, Belfast)

phylogenetics

Installing phyx without sudo

Tanglegrams can be misleading

blog

Goodbye Wordpress

cuda

Easy debugging of C/C++/CUDA python extensions

music

Mercury Prize 2023