Blog Archives

PubMed Publication Date: what is it, exactly?

September 23, 2014
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PubMed Publication Date: what is it, exactly?

File this one under “has troubled me (and others) for some years now, let’s try to resolve it.” Let’s use the excellent R/rentrez package to search PubMed for articles that were retracted in 2013. 117 articles. Now let’s fetch the records in XML format. Next question: which XML element specifies the “Date of publication” (PDAT)?

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Ebola, Wikipedia and data janitors

September 21, 2014
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Ebola, Wikipedia and data janitors

Sometimes, several strands of thought come together in one place. For me right now, it’s the Wikipedia page “Ebola virus epidemic in West Africa”, which got me thinking about the perennial topic of “data wrangling”, how best to provide public data and why I can’t shake my irritation with the term “data science”. Not to

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Venn figures go wrong

August 12, 2014
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Venn figures go wrong

I thought nothing could top the classic “6-way Venn banana”, featured in The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. That is until I saw Figure 3 from Compact genome of the Antarctic midge is likely an adaptation to an extreme environment. What’s odd is that Figure 2 in the latter paper

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When life gives you coloured cells, make categories

August 5, 2014
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When life gives you coloured cells, make categories

Let’s start by making one thing clear. Using coloured cells in Excel to encode different categories of data is wrong. Next time colleagues explain excitedly how “green equals normal and red = tumour”, you must explain that (1) they have sinned and (2) what they meant to do was add a column containing the words

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Converting a spreadsheet of SMILES: my first OSM contribution

June 30, 2014
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Converting a spreadsheet of SMILES: my first OSM contribution

I’ve long admired the work of the Open Source Malaria Project. Unfortunately time and “day job” constraints prevent me from being as involved as I’d like. So: I was happy to make a small contribution recently in response to this request for help: Can anyone help @O_S_M to convert this spreadsheet ( malaria.ourexperiment.org/biological_dat…) into chemical

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This is why code written by scientists gets ugly

May 13, 2014
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This is why code written by scientists gets ugly

There’s a lot of discussion around why code written by self-taught “scientist programmers” rarely follows what a trained computer scientist would consider “best practice”. Here’s a recent post on the topic. One answer: we begin with exploratory data analysis and never get around to cleaning it up. An example. For some reason, a researcher (let’s

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A minor update to my “apply functions” post

February 27, 2014
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A minor update to my “apply functions” post

One of my more popular posts is A brief introduction to “apply” in R. Come August, it will be four years old. Technology moves on, old blog posts do not. So: thanks to BioStar user zx8754 for pointing me to this Stack Overflow post, in which someone complains that the code in the post does

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Box plots. Like box plots, only…box plots.

February 2, 2014
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Box plots. Like box plots, only…box plots.

On a rare, brief holiday (here and here, if you’re interested; both highly-recommended), I make the mistake of checking my Twitter feed: paging @neilfws . . . RT @psudmant: Ground breaking new methods from @naturemethods – boxplots – no rly nature.com/nmeth/journal/…— Chris Miller (@chrisamiller) January 30, 2014 This points me to BoxPlotR. It draws box

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BLATting the internet: the most frequent gene?

January 23, 2014
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BLATting the internet: the most frequent gene?

I enjoyed this story from the OpenHelix blog today, describing a Microsoft Research project to mine DNA sequences from web pages and map them to UCSC genome builds. Laura DeMare asks: what was the most-hit gene? Most hit gene? APOE? MT @GenomeBrowser We BLATed the Internet! DNA sequences from 40 billion webpages mapped to hg19

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Quilt plots. Like heat maps, only…heat maps

January 15, 2014
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Quilt plots. Like heat maps, only…heat maps

Stephen tweets: Quilt Plots: A Simple Tool for the #Visualisation of Large Epidemiological Data buff.ly/1doSx4X— Stephen Rudd (@SAGRudd) January 15, 2014 Quilt plots. Sounds interesting. The link points to a short article in PLoS ONE, containing a table and a figure. Here is Figure 1. If you looked at that and thought “Hey, that’s a

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