Posts Tagged ‘ web resources ’

Popular topics at the BioStar Q&A site

August 23, 2011
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Popular topics at the BioStar Q&A site

Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question is “How to find SNPs”, then

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ISMB coverage on Twitter? It’s possible there was…

July 31, 2011
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ISMB coverage on Twitter? It’s possible there was…

Peter writes: I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on

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GEO database: curation lagging behind submission?

August 30, 2010
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GEO database: curation lagging behind submission?

I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the issue, using the Bioconductor GEOmetadb

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I’d be more than happy with the unlinked data web

April 14, 2010
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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) # "Date" "TimeUTC" "Latitude" "Longitude" "Magnitude" "Depth" # number of recent quakes nrow(quakes) #

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The Life Scientists at FriendFeed: 2009 summary

December 23, 2009
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The Life Scientists at FriendFeed: 2009 summary

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

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APIs: I wish the life sciences would learn from social networks

December 10, 2009
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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_date(d) if d

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A brief survey of R web interfaces

November 29, 2009
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A brief survey of R web interfaces

I’m looking at ways to provide access to R via a web application. First rule: see what’s available first, before you reinvent the wheel. It’s not pretty. From the R Web Interfaces FAQ: Software Brief notes Rweb Page last updated 1999. Of the 3 example links on the page one ran very slowly, the second not at

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An R Wiki

April 21, 2008
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An R Wiki

It’s been ages since I visited the R website, so I don’t know how long they’ve had a wiki. It’s built using DokuWiki, one of my personal favourites. This is a great leap forward for R documentation, which is somewhat notorious for being (a) difficult to find and (b) difficult to understand when you find

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