MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'geo'. Sat, 03 Sep 2011 02:39:49 +0100 http://www.medworm.com/index.php?rid=4872060&cid=t_316952_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FT5PxUyB1Bis%2F By Julian SanchezBarack Obama’s AutoPen has signed another four-year extension of three Patriot Act powers, but one silver lining of this week’s lopsided battle over the law is that mainstream papers like The New York Times have finally started to take note of the growing number of senators who have raised an alarm over a “secret interpretation” of Patriot’s “business records” authority (aka Section 215). It would appear to be linked to a “sensitive collection program” referenced by a Justice Department official at hearings during the previous reauthorization debate—one that would be disrupted if 215 orders were restricted to the records of suspected terrorists, their associates, or their “activities” (e.g., large purchase... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=4872060 Fri, 27 May 2011 17:25:23 +0100 4872060 http://www.medworm.com/index.php?rid=4036789&cid=t_316952_118_f&fid=39279&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffoxepractice%2F%7E3%2FYltNdizeevg%2Fgame-dynamics-healthcare-hipaa As a result of bringing location-based social networking to the masses, Facebook Places will also bring us game dynamics. This will have huge implications for local businesses, including hospitals, medical practices and other healthcare providers. Let’s look at the implications and opportunities that the adoption of this technology will have for medical providers. What are game dynamics? If you’ve got 10 minutes, you may want to watch the highly distributed TED video “The Game Layer on Top of the World” (scroll to the bottom of this article for the video). In short, it’s just a fancy name for a range of incentives that reward desired behavior. We’ve had game dynamics in the “real world” for a long time, but it has recently been taken to ... Fox ePractice blogs http://www.medworm.com/rss/comments.php?id=4036789 Wed, 06 Oct 2010 14:07:12 +0100 4036789 http://www.medworm.com/index.php?rid=3915213&cid=t_316952_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F30%2Fgeo-database-curation-lagging-behind-submission%2F GSE and GDS records in GEOmetadb by date 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 package and ggplot2. Left, the resulting image – click for larger version. Is the curation effort keeping up with user submissions? A little difficult to say, since GEOmetadb curation seems to have its own issues: (1) why do GDS records stop in 2008? (2) why do GDS (curated) records begin earlier than GSE (submitted) records? library(GEOmetadb) library(ggplot2) # update database if required usi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3915213 Mon, 30 Aug 2010 08:11:16 +0100 3915213 http://www.medworm.com/index.php?rid=3216663&cid=t_316952_109_f&fid=38950&url=http%3A%2F%2Fwww.shockmd.com%2F2010%2F01%2F28%2Fthe-formula-for-life%2F Where you live: It impacts your health as much as diet and genes do, but it’s not part of your medical records. Bill Davenhall shows how overlooked government geo-data (from local heart-attack rates to toxic dumpsite info) can mesh with mobile GPS apps to keep doctors in the loop. Call it “geo-medicine.” Related posts:Charles Darwin And The Tree Of Life BBC’s Darwin season featured ‘Charles Darwin and the Tree... Evolution of Life in 60 Seconds The Evolution of Life in 60 Seconds is an... Google Apps Tricks If your like me, having 5 e-mail accounts, a... Related posts brought to you by Yet Another Related Posts Plugin. (Source: Dr Shock MD PhD) Dr Shock MD PhD blogs http://www.medworm.com/rss/comments.php?id=3216663 Thu, 28 Jan 2010 07:03:53 +0100 3216663 http://www.medworm.com/index.php?rid=3212505&cid=t_316952_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F27%2Fclustering-geo-samples-by-title-briefly-revisited%2F So, we had a brief discussion regarding my previous post and clearly the statement: The longest key for which values exist classifies your titles does not hold true for all cases. Not that I ever said that it did! I remind you that this blog is a place for the half-formed ideas that spill out of my head, not an instruction manual. Let’s look, for example, at GSE19318. This GEO series comprises 2 platforms: one for dog (10 samples) and one for humans (1 sample), with these sample titles: ['Dog-tumor-81705', 'Dog-tumor-78709', 'Dog-tumor-88012', 'Dog-tumor-8888302', 'Dog-tumor-209439', 'Dog-tumor-212227', 'Dog-tumor-48', 'Dog-tumor-125', 'Dog-tumor-394', 'Dog-tumor-896', 'Human-tumor'] Run that through the Ruby code in my last post and we get: {"Dog-tumor-48"=>["... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3212505 Wed, 27 Jan 2010 01:29:56 +0100 3212505 http://www.medworm.com/index.php?rid=3201861&cid=t_316952_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F24%2Fthinking-algorithmically-clustering-geo-samples-by-title%2F Today’s challenge. Take a look at this array, which contains the “title” field for the 6 samples from GSE1323, a series in the GEO microarray database: ['SW-480-1','SW-480-2','SW-480-3','SW-620-1','SW-620-2','SW-620-3'] Humans are very good at classification. Almost instantly, you’ll see that there are 2 classes, “SW-480″ and “SW-620″, each with 3 samples. How can we write a program to do the same job? I’m sure that for those with formal training in computer science and algorithms, this is pretty trivial. The rest of us have to figure it out from first principles. Here’s what I did, in words: # Imagine that you have 2 titles: "abc1" and "abc2" # Take the first character - call it the key, call the remaining... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3201861 Sun, 24 Jan 2010 05:03:00 +0100 3201861 http://www.medworm.com/index.php?rid=3153558&cid=t_316952_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F08%2Fsamples-per-seriesdataset-in-the-ncbi-geo-database%2F 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 GEOmetadb package, available from Bioconductor. The R code first, then some explanation: # install GEOmetadb source("http://bioconductor.org/biocLite.R") biocLite("GEOmetadb") library(GEOmetadb) # connect to database getSQLiteFile() con <- dbConnect(SQLite(), "GEOmetadb.sqlite") # count samples per GDS gds.count <- dbGetQuery(con, "select gds,sample_count from gds") gds.count[1:5,] # first 5 results... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3153558 Fri, 08 Jan 2010 01:01:09 +0100 3153558 http://www.medworm.com/index.php?rid=3079512&cid=t_316952_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F11%2Fapis-i-wish-the-life-sciences-would-learn-from-social-networks%2F 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 =~ /(\d{4}-\d{2}-\d{2})T(\d{2}:\d{2}:\d{2})Z/ return "#{$1},#{$2}" else return d end end def count_items(i) if i.nil? return 0 else return i.count end end n = ARGV[0] u = "http://friendfeed-api.com/v2/feed/the-life-scientists?start=#{n}" f = open(u).read j = JSON.parse(f) j.each_pair do |k,v| if k == "entries" v.each do |entry| date = format_date(entry['date']) likes = count_it... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3079512 Fri, 11 Dec 2009 02:50:49 +0100 3079512 http://www.medworm.com/index.php?rid=1373612&cid=t_316952_93_f&fid=36200&url=http%3A%2F%2Fblog.jammedph.com%2Ffree-tools-to-monitor-your-website%2F You can’t just put your website on the net with right keywords and all the right touches and expect your traffic and ranking will remain constant. As the web is an ever changing landscape, you have to keep track of your own web results like what is happening with the competition and also the best and highest ranked sites. There are many useful tools to help you find out what exactly is happening. 1. A tool which you can use to test your own website links or other websites for broken links: http://home.snafu.de/tilman/xenulink.html 2. With this tool you can check search engines for the number of back links to your URL i.e. other web pages linking to your site: http://www.digitalpoint.com/tools/backlinks/ 3. It sometimes becomes important to know where the servers of your hosting company ... Jammed: Full into Capacity blogs http://www.medworm.com/rss/comments.php?id=1373612 Tue, 15 Apr 2008 11:09:16 +0100 1373612