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<!DOCTYPE html> <html> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width initial-scale=1" /> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <title>alimanfoo</title> <meta name="description" content="Alistair Miles' blog.">  <meta property="og:url" content="http://alimanfoo.github.io/"> <meta property="og:type" content="website"> <meta property="og:title" content="alimanfoo"> <meta property="og:description" content="Alistair Miles' blog.">  <meta name="twitter:card" content="summary_large_image"> <meta property="twitter:domain" content="http://alimanfoo.github.io"> <meta property="twitter:url" content="http://alimanfoo.github.io/"> <meta name="twitter:title" content="alimanfoo"> <meta name="twitter:description" content="Alistair Miles' blog."> <link rel="stylesheet" href="/css/main.css"> <link rel="canonical" href="http://alimanfoo.github.io/"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css"> <script src="/assets/require.js"></script> </head> <body> <header class="site-header"> <div class="wrapper"> <a class="site-title" href="/">alimanfoo</a> <nav class="site-nav"> <a href="#" class="menu-icon"> <svg viewBox="0 0 18 15"> <path fill="#424242" d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.031C17.335,0,18,0.665,18,1.484L18,1.484z"/> <path fill="#424242" d="M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0c0-0.82,0.665-1.484,1.484-1.484 h15.031C17.335,6.031,18,6.696,18,7.516L18,7.516z"/> <path fill="#424242" d="M18,13.516C18,14.335,17.335,15,16.516,15H1.484C0.665,15,0,14.335,0,13.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.031C17.335,12.031,18,12.696,18,13.516L18,13.516z"/> </svg> </a> <div class="trigger"> <a class="page-link" href="/">Blog</a> <a class="page-link" href="/publications/">Science</a> <a class="page-link" href="/software/">Code</a> <a class="page-link" href="/data/">Data</a> <a class="page-link" href="/team/">Team</a> <a class="page-link" href="/about/">About</a> </div> </nav> </div> </header> <div class="page-content"> <div class="wrapper"> <div class="home"> <ul class="post-list"> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jan 6, 2025</span> <h2> <a class="post-link" href="/2025/01/06/vector-genomics-in-2024.html"> A vintage year for African malaria vector genomics </a> </h2> <p><em>Scientific highlights from 2024.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Nov 16, 2024</span> <h2> <a class="post-link" href="/2024/11/16/llm-use-case.html"> A coding assistant for genomic data analysis? </a> </h2> <p><em>AI coding assistants are getting very good. Would it be possible to create an AI assistant to support generation of code to analyse genomic data on malaria mosquitoes?</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Oct 18, 2024</span> <h2> <a class="post-link" href="/2024/10/18/faster-neighbour-joining.html"> Faster neighbour-joining <img src=/src/2024-10-18-faster-neighbour-joining/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>A new Python package called anjl provides fast implementations of the neighbour-joining algorithm and interactive plotting of unrooted trees.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 5, 2024</span> <h2> <a class="post-link" href="/2024/09/05/kenya-coluzzii-njt.html"> Anopheles coluzzii in Kenya - neighbour-joining tree analysis <img src=/src/2024-09-05-kenya-coluzzii-njt/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>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.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Aug 20, 2024</span> <h2> <a class="post-link" href="/2024/08/20/jupyter-blogging.html"> Blogging with Jekyll, Jupyter notebooks and interactive plots (Plotly, Bokeh) <img src=/src/2024-08-20-jupyter-blogging/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>How to create blog posts from Jupyter notebooks which include interactive plots made with Plotly or Bokeh.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Aug 16, 2024</span> <h2> <a class="post-link" href="/2024/08/16/diplotype-clustering.html"> Diplotype clustering <img src=/src/2024-08-16-diplotype-clustering/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Introduces advanced diplotype clustering, a new function in the malariagen_data Python package for investigating insecticide resistance mutations.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jul 3, 2024</span> <h2> <a class="post-link" href="/2024/07/03/nairobi.html"> Arthropod Genomics Symposium 2024 <img src=/assets/2024-07-03-nairobi.jpeg width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Highlights from the Arthropod Genomics Symposium in Nairobi - gene drives, microbiome, genome assemblies and insecticide resistance.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 7, 2024</span> <h2> <a class="post-link" href="/2024/06/07/vobs-landing-page.html"> The Malaria Vector Genome Observatory is online <img src=/src/2024-06-07-vobs-landing-page/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Introducing a new web page for the Malaria Vector Genome Observatory providing an entry point to data, training, software, research and more.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Nov 16, 2023</span> <h2> <a class="post-link" href="/2023/11/16/vobs20k.html"> 20,000 Anopheles mosquito genomes <img src=/assets/2023-11-16-vobs20k/network.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>The Malaria Vector Genome Observatory now contains analysis-ready data from whole-genome sequencing of 22,015 Anopheles mosquitoes.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Mar 10, 2023</span> <h2> <a class="post-link" href="/2023/03/10/data-analysis-training.html"> Training course in data analysis for genomic surveillance of African malaria vectors <img src=/src/2023-03-10-data-analysis-training/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>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.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Nov 9, 2022</span> <h2> <a class="post-link" href="/2022/11/09/kigali.html"> Kigali, September 2022 <img src=/assets/2022-11-09-kigali.jpeg width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Reflections from the PAMCA Conference 2022 in Kigali, Rwanda.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Feb 26, 2022</span> <h2> <a class="post-link" href="/2022/02/26/phd.html"> Trust me, I'm a doctor! <img src=/src/2022-02-26-phd/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>6 years, 2 babies and a pandemic later, I finally graduated as a Doctor of Philosophy. It was a sunny, winter's day in Oxford, and I got to share the experience with my wife and eldest daughter, it was a real treat. Here is a brief overview of my thesis and a few personal reflections on doing a PhD later in life.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 14, 2021</span> <h2> <a class="post-link" href="/2021/06/14/gem-ag3.html"> Ag1000G phase 3 lightning talk at GEM 2021 <img src=/assets/2021-06-14-gem-ag3.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>A brief introduction to the open genomic data resources on malaria mosquitoes being created in phase 3 of the Anopheles gambiae 1000 Genomes Project.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Mar 22, 2021</span> <h2> <a class="post-link" href="/dask/2021/03/22/dask-memory-thought.html"> Dask thought: distributed clusters and worker memory/storage <img src=/assets/2021-03-22-dask-memory-thought.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Some thoughts about Dask clusters and memory management.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Mar 16, 2021</span> <h2> <a class="post-link" href="/2021/03/16/xarray-query.html"> Querying multidimensional data with xarray <img src=/src/2021-03-16-xarray-query/image.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>A new query() method for the xarray Dataset class.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Feb 16, 2021</span> <h2> <a class="post-link" href="/2021/02/16/vgsc.html"> On the evolution of pyrethroid target-site resistance <img src=/assets/2021-02-16-vgsc.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>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.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Aug 8, 2019</span> <h2> <a class="post-link" href="/2019/08/08/anopheles-cnvs.html"> Insecticide resistance gene copy number variation in malaria mosquitoes <img src=/assets/2019-08-08-anopheles-cnvs.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Introduces recent work on copy number variation by the Anopheles gambiae 1000 Genomes Project.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 19, 2019</span> <h2> <a class="post-link" href="/zarr/specs/2019/06/19/zarr-v3-update.html"> Zarr protocol v3 design update <img src=/assets/2019-06-19-zarr-v3-update.png width="400px" style="display: block; max-width: 95%" /> </a> </h2> <p><em>Shares some slides summarising the current state of exploratory work on the Zarr v3 protocol spec.</em></p> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">May 23, 2019</span> <h2> <a class="post-link" href="/zarr/python/release/2019/05/23/zarr-2.3-release.html"> Zarr Python 2.3 release </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Aug 1, 2018</span> <h2> <a class="post-link" href="/2018/08/01/genomics-modelling-postdoc.html"> Senior post-doc in malaria vector genomics and modelling </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Apr 12, 2018</span> <h2> <a class="post-link" href="/2018/04/12/zarr-tech-dive.html"> Zarr 2.2 tech dive </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Apr 9, 2018</span> <h2> <a class="post-link" href="/2018/04/09/selecting-variants.html"> Selecting variants and samples </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 25, 2017</span> <h2> <a class="post-link" href="/2017/06/25/panoptes-videos.html"> Web-based exploration of genome variation data </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 14, 2017</span> <h2> <a class="post-link" href="/2017/06/14/read-vcf.html"> Extracting data from VCF files </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">May 18, 2017</span> <h2> <a class="post-link" href="/2017/05/18/installing-python.html"> Installing Python for data analysis </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Feb 14, 2017</span> <h2> <a class="post-link" href="/2017/02/14/mendelian-transmission.html"> Mendelian transmission </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jan 25, 2017</span> <h2> <a class="post-link" href="/2017/01/25/vgsc-gene-models.html"> VGSC gene models </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jan 23, 2017</span> <h2> <a class="post-link" href="/2017/01/23/go-faster-python.html"> Go faster Python </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Oct 4, 2016</span> <h2> <a class="post-link" href="/2016/10/04/plotting-african-ecosystems.html"> Plotting African ecosystems </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 21, 2016</span> <h2> <a class="post-link" href="/2016/09/21/genotype-compression-benchmark.html"> Genotype compressor benchmark </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 9, 2016</span> <h2> <a class="post-link" href="/2016/09/09/zarr-2-groups-filters.html"> Zarr 2 - groups, filters and Zstandard </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 21, 2016</span> <h2> <a class="post-link" href="/2016/06/21/understanding-pbwt.html"> Understanding PBWT </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Jun 10, 2016</span> <h2> <a class="post-link" href="/2016/06/10/scikit-allel-tour.html"> A tour of scikit-allel </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">May 31, 2016</span> <h2> <a class="post-link" href="/2016/05/31/matplotlib-xkcd.html"> XKCD-style plots </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">May 16, 2016</span> <h2> <a class="post-link" href="/2016/05/16/cpu-blues.html"> CPU blues </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Apr 14, 2016</span> <h2> <a class="post-link" href="/2016/04/14/to-hdf5-and-beyond.html"> To HDF5 and beyond </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Dec 23, 2015</span> <h2> <a class="post-link" href="/2015/12/23/mosquito-genomes.html"> Mosquito genomes and malaria control, the podcast </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Oct 13, 2015</span> <h2> <a class="post-link" href="/2015/10/13/parasite-crosses.html"> Genetic variation in parasite crosses </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 28, 2015</span> <h2> <a class="post-link" href="/2015/09/28/fast-pca.html"> Fast PCA </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 21, 2015</span> <h2> <a class="post-link" href="/2015/09/21/estimating-fst.html"> Estimating F<sub>ST</sub> </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 15, 2015</span> <h2> <a class="post-link" href="/2015/09/15/introducing-scikit-allel.html"> Introducing scikit-allel </a> </h2> </li> <li style="border-bottom: 1px solid #e8e8e8;"> <span class="post-meta">Sep 15, 2015</span> <h2> <a class="post-link" href="/2015/09/15/blog-migrated.html"> Blog, migrated </a> </h2> </li> </ul> <p class="rss-subscribe">subscribe <a href=" /feed.xml">via RSS</a></p> </div> </div> </div> <footer class="site-footer"> <div class="wrapper"> <div class="footer-col-wrapper"> <div class="footer-col footer-col-1"> <ul class="contact-list"> <li>漏 Alistair 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