Publications by nsaunders
APIs: I wish the life sciences would learn from social networks
I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_...
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The Life Scientists at FriendFeed: 2009 summary
The Life Scientists 2009 It’s Christmas Eve tomorrow and so I declare the year over. My Christmas gift to you is a summary of activity in 2009 at the FriendFeed Life Scientists group. It’s crafted using R + Ruby, with raw data and some code snippets available. If you want to see the most popular items from the group this year, head down to...
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Samples per series/dataset in the NCBI GEO database
Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in, but it won’t come out. However, there is an alternative: the G...
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A new twist on the identifier mapping problem
Yesterday, Deepak wrote about BridgeDB, a software package to deal with the “identifier mapping problem”. Put simply, biologists can name a biological entity in any way that they like, leading to multiple names for the same object. Easily solved, you might think, by choosing one identifier and sticking to it, but that’s apparently way too...
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From the “blogosphere”? Hardly.
I generally skip over “From the Blogosphere”, a (mostly) weekly-summary of one or two blog posts in Nature’s “Authors” section (here is the latest). Why? Well, I’ve always suspected that the title is rather misleading. Now, I have the hard numbers to prove it. My feed reader contains an archive of 128 articles, dating back to May 1...
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BioMart (and biomaRt)
I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values – for example, HGNC symb...
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Plotting “time of day” data using ggplot2
William asks: How can I make a graph that looks like this, “tweet density” style, showing time intervals? He then helpfully describes his input data: a CSV file with headers “time started, time finished, date”. Here’s a simple CSV file, tasks.csv: task,date,start,end task1,2010-03-05,09:00:00,13:00:00 task2,2010-03-06,10:00:00,15:00...
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I’d be more than happy with the unlinked data web
Visit this URL and you’ll find a perfectly-formatted CSV file containing information about recent earthquakes. A nice feature of R is the ability to slurp such a URL straight into a data frame: quakes <- read.csv("http://neic.usgs.gov/neis/gis/qed.asc", header = T) colnames(quakes) # [1] "Date" "TimeUTC" "Latitude" "Longitude" "Magnitu...
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Getting your web application and R(Apache) to talk to each other
Here’s the situation. Web applications, built using a framework (e.g. Rails, Django) are great for fetching data from a database and rendering it. They’re not so great for crunching and charting the data. Conversely, R is great for crunching and charting, but doesn’t make for a great web application. Index view for values The idea then, ...
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Experiments with igraph
Networks – social and biological – are all the rage, just now. Indeed, a recent entry at Duncan’s QOTD described the “hairball” network representation as the dominant cultural icon in molecular biology. I’ve not had occasion to explore networks “professionally”, but have always been fascinated by both networks and the tools used ...
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