Sequencing DNA with Linux Cores and Nanopores

C1 | Thu 24 Jan | 10:40 a.m.–11:25 a.m.


Presented by

  • David Eccles
    @gringene_bio
    http://www.gringene.org

    David Eccles is a freelance bioinformatician currently working for a number of different research groups at the Malaghan Institute of Medical Research. He has a background in genetics, logic & computation, and biology, with a foreground in theoretical genetics, nanopore sequencing, and 3D printing. Observations about novel interpretations of data have encouraged David to hunt for comparative statistics that don't need statistics, and explore better ways of investigating and visualising raw data to explain why mathematical models don't always match the harsh reality of biology. David uses free and open source software, and is used to the ecosystem of bug reporting and constant, living software development. He is an advocate for diverse, open, transparent research that shines a light through the cobwebs of academic rigidity.

Abstract

The Oxford Nanopore MinION is a small stapler-sized device that is quietly disrupting the way that the world looks at the world. Despite what TV shows will tell you, deoxyribose nucleic acid (DNA) is not a bunch of letters on a computer screen. Those letters represent a physical thing: long, stringy whiteish stuff that frequently has a gel-like consistency and an amazing ability to clump together with itself. The MinION is a DNA sequencer. DNA sequencing is the process of turning the physical thing of DNA into a model of that thing on a computer. Using this pocket-sized device, researchers have been able to sequence DNA in the jungle, at the bottom of the ocean, in Antarctica, and on board the International Space Station. For LCA, the challenge will be to prepare, sequence, and analyse a sample of DNA over the course of single talk, with no external power source (apart from the laptop battery), and using freely available software and DNA sequence databases. LinuxConf attendees will be given access to the DNA sequences produced during the talk, and are free to add their own creative interpretations of long strings of four different letters.