alimanfoo

Oct 18, 2024
Faster neighbour-joining

A new Python package called anjl provides fast implementations of the neighbour-joining algorithm and interactive plotting of unrooted trees.
Sep 5, 2024
Anopheles coluzzii in Kenya - neighbour-joining tree analysis

Replicates the neighbour-joining tree analysis from Kamau et al. (2024) on Anopheles coluzzii in northwestern Kenya and demonstrates the plot_njt() function in the malariagen_data Python package.
Aug 20, 2024
Blogging with Jekyll, Jupyter notebooks and interactive plots (Plotly, Bokeh)

How to create blog posts from Jupyter notebooks which include interactive plots made with Plotly or Bokeh.
Aug 16, 2024
Diplotype clustering

Introduces advanced diplotype clustering, a new function in the malariagen_data Python package for investigating insecticide resistance mutations.
Jul 3, 2024
Arthropod Genomics Symposium 2024

Highlights from the Arthropod Genomics Symposium in Nairobi - gene drives, microbiome, genome assemblies and insecticide resistance.
Jun 7, 2024
A new landing page for the Malaria Vector Genome Observatory

Introduces malariagen.net/vobs - a new web page for the Malaria Vector Genome Observatory and an entry point to data, training, software, research and more.
Mar 10, 2023
Training course in data analysis for genomic surveillance of African malaria vectors

This post introduces a new training course and explains some of the rationale and technology choices we made to create, publish and deliver the course online.
Nov 9, 2022
Kigali, September 2022

Reflections from the PAMCA Conference 2022 in Kigali, Rwanda.
Jun 14, 2021
Ag1000G phase 3 lightning talk at GEM 2021

A brief introduction to the open genomic data resources on malaria mosquitoes being created in phase 3 of the Anopheles gambiae 1000 Genomes Project.
Mar 22, 2021
Dask thought: distributed clusters and worker memory/storage

Some thoughts about Dask clusters and memory management.
Mar 16, 2021
Querying multidimensional data with xarray

A new query() method for the xarray Dataset class.
Feb 16, 2021
On the evolution of pyrethroid target-site resistance

There are multiple double- and triple-mutant combinations in the Vgsc gene which I think we should be more concerned about, and they are evolving in different ways.
Aug 8, 2019
Insecticide resistance gene copy number variation in malaria mosquitoes

Introduces recent work on copy number variation by the Anopheles gambiae 1000 Genomes Project.
Jun 19, 2019
Zarr protocol v3 design update

Shares some slides summarising the current state of exploratory work on the Zarr v3 protocol spec.
May 23, 2019
Zarr Python 2.3 release
Aug 1, 2018
Senior post-doc in malaria vector genomics and modelling
Apr 12, 2018
Zarr 2.2 tech dive
Apr 9, 2018
Selecting variants and samples
Jun 25, 2017
Web-based exploration of genome variation data
Jun 14, 2017
Extracting data from VCF files
May 18, 2017
Installing Python for data analysis
Feb 14, 2017
Mendelian transmission
Jan 25, 2017
VGSC gene models
Jan 23, 2017
Go faster Python
Oct 4, 2016
Plotting African ecosystems
Sep 21, 2016
Genotype compressor benchmark
Sep 9, 2016
Zarr 2 - groups, filters and Zstandard
Jun 21, 2016
Understanding PBWT
Jun 10, 2016
A tour of scikit-allel
May 31, 2016
XKCD-style plots
May 16, 2016
CPU blues
Apr 14, 2016
To HDF5 and beyond
Dec 23, 2015
Mosquito genomes and malaria control, the podcast
Oct 13, 2015
Genetic variation in parasite crosses
Sep 28, 2015
Fast PCA
Sep 21, 2015
Estimating F_ST
Sep 15, 2015
Introducing scikit-allel
Sep 15, 2015
Blog, migrated