Tag Archives: bioinformatics

Inference and informatics in a ‘sequenced’ world

Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs. University of Reading, 2nd August 2017 Slides [SlideShare]: cc-by-nd Tweet … Continue reading

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Using field-based DNA sequencing to accelerate phylogenomics

Invited seminar at the Department of Zoology, Oxford University, 30th November 2016. Summary of our field-based real-time phylogenomics (MinION DNA sequencing) experiments this year, and applicability to broad-scale tree-of-life phylogenomics and macroevolutionary biology. Slides [SlideShare]: cc-by-nd Tweet this Digg Post … Continue reading

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Why aren’t we benchmarking bioinformatics?

Talk presented at the #bench16 (benchmarking) symposium at KCL, London, Wed 20th April 2016. Funded by the SSI. Slides (Slideshare – cc-by-nd) Tweet this Digg Post to LinkedIn Slashdot Stumble This

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Copying LOADS of files from a folder of LOADS *AND* LOADS more in OSX

Quick one this, as it’s a tricky problem I keep having to Google/SO. So I’m posting here for others but mainly myself too! Here’s the situation: you have a folder (with, ooh, let’s say 140,000 separate MinION reads, for instance…) … Continue reading

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How to fake an OSX theme appearance in Linux Ubuntu MATE

I’ve recently been fiddling about and trying to fake an OSX-style GUI appearance in Linux Ubuntu MATE (15.04). This is partly because I prefer the OSX GUI (let’s be honest) and partly because most of my colleagues are also Mac … Continue reading

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Messing about with the MinION

Molecular phylogenetics – uncovering the history of evolution using signals in organisms’ genetic sequences – is a powerful science, the latest expression of the human desire to understand our common origins. But for all its achievements, I’d always felt something … Continue reading

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Real-time Phylogenomics

General science talk about the potential of real-time phylogenomics, delivered at the Jodrell Lecture Theatre, Kew Gardens, November 2nd 2015 Slides [SlideShare]: cc-by-nc-nd Tweet this Digg Post to LinkedIn Slashdot Stumble This

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Omics in extreme Environments (Lightweight bioinformatics)

Presentation on lightweight bioinformatics (Raspi / cloud computing) for real-time field-based analyses. Presented at iEOS2015, St. Andrews, 3-6th July 2015. Slides [SlideShare]: cc-by-nc-nd Tweet this Digg Post to LinkedIn Slashdot Stumble This

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Parsing numbers from multiple formats in Java

We were having a chat over coffee today and a question arose about merging data from multiple databases. At first sight this seems pretty easy, especially if you’re working with relational databases that have unique IDs (like, uh, a Latin … Continue reading

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HYPHY Hack: Passing arguments to HYPHY for phylogenetics using the command-line

[ Important update, 2017-Feb-07 ] [ This solution, already a bit hacky, should now be considered a last-resort. Sergei and colleague Stephen Weaver have suggested a much more elegant solution; see: https://github.com/veg/hyphy/issues/522. You’ll still have to dive into the batch file you want to … Continue reading

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