Oct 4, 2016. Sep 21, 2016. Sep 9, 2016. Zarr 2 - groups, filters and Zstandard. Jun 21, 2016. Jun 10, 2016. A tour of scikit-allel. May 31, 2016. May 16, 2016. 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. Sep 21, 2015. Sep 15, 2015. Sep 15, 2015.
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Alistair Miles | alimanfoo.github.io Reviews
https://alimanfoo.github.io
Oct 4, 2016. Sep 21, 2016. Sep 9, 2016. Zarr 2 - groups, filters and Zstandard. Jun 21, 2016. Jun 10, 2016. A tour of scikit-allel. May 31, 2016. May 16, 2016. 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. Sep 21, 2015. Sep 15, 2015. Sep 15, 2015.
alimanfoo.github.io
CPU blues
http://alimanfoo.github.io/2016/05/16/cpu-blues.html
May 16, 2016. Notes on reducing I/O bottlenecks in parallel computations with Dask. When I’m analysing data I tend to keep one eye on the system monitor at the top of my screen. The height of the green bar tells me how much RAM I’m using and the height of the blue bar tells me how much CPU. One solution I really like is Dask. Of some of the basic genetic data transformations I use every day. I then ran these on some data from the Ag1000G project. Dask 0.11.1 scikit-allel 1.0.3. 6553, 200, 2). The h5py li...
Reading
http://alimanfoo.github.io/reading
This page is a reading diary, inspired by #365papers. Sort by first author. Sort by date read. Minimum Spanning Trees and Single Linkage Cluster Analysis. Journal of the Royal Statistical Society. Series C (Applied Statistics). Statistics; clustering; networks. Making sense of genomic islands of differentiation in light of speciation. Journal club; speciation; heliconius; crows; sticklebacks; review. Linkage disequilibrium- understanding the evolutionary past and mapping the medical future. Identificatio...
A tour of scikit-allel
http://alimanfoo.github.io/2016/06/10/scikit-allel-tour.html
A tour of scikit-allel. Jun 10, 2016. This notebook contains a brief tour of some exploratory analyses that can be performed on large-scale genome variation data using scikit-allel. In combination with general purpose Python scientific libraries such as numpy. Project (phase 1) we have whole-genome sequence data from 765 individual mosquitoes collected from 8 different countries across Africa. We have used a standard approach. The goal of this tour is to give a flavour of:. How much coding is required.
Zarr 2 - groups, filters and Zstandard
http://alimanfoo.github.io/2016/09/09/zarr-2-groups-filters.html
Zarr 2 - groups, filters and Zstandard. Sep 9, 2016. Recently I’ve been working on Zarr. A Python package providing chunked, compressed storage for numerical arrays. I’ve just released Zarr version 2. Which adds two new major features: groups. It also brings support for Zstandard. This post provides a brief tour of what’s new. Zarr 2.1.1 blosc 1.11.1. Zarr is heavily inspired by HDF5. Here’s how to create a group with Zarr:. Group(/, 0) store: DictStore. If you are familiar with h5py. In the examples abo...
Genotype compressor benchmark
http://alimanfoo.github.io/2016/09/21/genotype-compression-benchmark.html
Sep 21, 2016. This blog post benchmarks different compressors for use with genotype data from large-scale resequencing projects. TL;DR for speed you can’t beat Blosc LZ4, but Blosc Zstd Bitshuffle gives a very high compression ratio with good all-round performance. Why do I care about compression? Fast compression brings interactive analysis of genome variation data. The data used in this benchmark are genotype data from the Ag1000G project phase 1 AR3 data release. And can be downloaded via FTP. For the...
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Alistair Miles
Oct 4, 2016. Sep 21, 2016. Sep 9, 2016. Zarr 2 - groups, filters and Zstandard. Jun 21, 2016. Jun 10, 2016. A tour of scikit-allel. May 31, 2016. May 16, 2016. 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. Sep 21, 2015. Sep 15, 2015. Sep 15, 2015.
Alistair Miles | purl.org/net/aliman — Web technology for science & innovation
Purlorg/net/aliman — Web technology for science and innovation. 5 August, 2011. This is just a short post to say my colleagues and I have started a MalariaGEN Informatics Blog. That’s where I’m mostly posting at the moment. 17 January, 2011. Using SPARQL for Biological Data Integration – Reflections on openflydata.org and the FlyWeb Project. It’s now almost 18 months since the end of the FlyWeb project. And the development of the proof-of-concept site openflydata.org. Integrating Gene Expression Data.
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