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 'computing,'. Tue, 04 May 2010 18:20:39 +0100 http://www.medworm.com/index.php?rid=3526896&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Feh2LjAImkOU%2F Bradford Cross writes about datasets and data-driven startups. The entire post is full of nuggets, but one bit jumped out at me. Brad writes Data preprocessing, transformation, and systems engineering are normally the bulk of the work for data and research driven problems – all the more so when you are collecting data from disparate sources rather than using your own internal data When I wrote about Atul Butte’s talk at Sage Congress, this was where I was coming from. Bioinformaticians spend a lot of time dealing with data, and the transformation, etc needed to do with data coming from different sources. When you have a lot of publicly available data around, you have to be very good at the data handling and systems engineering. But once you overcome those barriers, you can star... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3526896 Sun, 02 May 2010 23:39:06 +0100 3526896 http://www.medworm.com/index.php?rid=3519624&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FAeGRxNfbGnM%2F The other day, I had the chance to see a great talk by Benjamin Black on how Cassandra handles replication and consistency. Slides by themselves do not do the talk justice, especially as there was a lot of great Q&A as well, but I think you’ll get a sense of how a good partition tolerant distributed system is set up. Introduction to Cassandra: Replication and Consistency View more presentations from benjaminblack. Related articles by Zemanta Scaling Twitter with Cassandra (slideshare.net) Cassandra reading list (spyced.blogspot.com) (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3519624 Fri, 30 Apr 2010 13:31:22 +0100 3519624 http://www.medworm.com/index.php?rid=3454003&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fipad-healthcare-game-changer There have been a lot of discussions on the net regarding the potential impact of the iPad in the healthcare sector. At this point, there is very little agreement with some pointing to the ubiquitous nature of the iPhone in healthcare as a foreshadowing of the iPad’s future impact, while others point to the modest uptake of tablet computing platforms as a precursor for minimal impact. Our 2 cents worth… We believe the iPad will see the biggest impact in two areas: medical education and patient-clinician communication. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3454003 Fri, 09 Apr 2010 13:00:58 +0100 3454003 http://www.medworm.com/index.php?rid=3433093&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Ffx9tV3aisso%2F At breakfast today I had a nice chat about bioinformatics, software, research and the entire ecosystem. In between bemoaning the lack of data architects and an appreciation for software and informatics, we talked about interesting ways to educate people about software and informatics. We ended up talking about github and virtual machines, and probably my favorite use case, Pete Skomoroch’s great work on building data intensive apps. Here are some of those tutorials Tracking trends with Hadoop and Hive on EC2 Grouping related trends with Hadoop and Hive The point of the discussion was this. If we could have more tutorials like this, essentially end-to-end tutorials with code and reference sites like trendingtopics.org but in a bioinformatics/genomics context, I am sure a whole bunch... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3433093 Fri, 02 Apr 2010 15:54:19 +0100 3433093 http://www.medworm.com/index.php?rid=3429227&cid=t_348399_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2010%2F04%2F01%2Fmental-illness-cured%2F After working on these issues for the past 150 years, Psych Central is pleased to announce a final, simple cure for mental illness. “Yes, it’s been a long-time in the making, but we finally figured out how to cure mental illness,” said Founder and CEO of Psych Central, Dr. John Grohol. “The final push came 6 months ago, when we realized we had not only discovered the single mental illness gene, but how to deactivate it with simple products found in most people’s homes.” The cure comes on the heels of over 150 years of mental illness being recognized as something needing treatment. Serious mental disorders — things such as depression, bipolar disorder, schizophrenia, anxiety and panic, ADHD — have long had a significant, negative impact in peo... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=3429227 Thu, 01 Apr 2010 14:55:36 +0100 3429227 http://www.medworm.com/index.php?rid=3424830&cid=t_348399_87_f&fid=36438&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FCato-at-liberty%2F%7E3%2FniqsTHnIV0w%2F By Julian SanchezImagine for a moment that all your computing devices had to run on code that had been written in 1986. Your smartphone is, alas, entirely out of luck, but your laptop or desktop computer might be able to get online using a dial-up modem. But you’d better be happy with a command-line interface to services like e-mail, Usenet, and Telnet, because the only “Web browsers” anyone’s heard of in 1986 are entomologists. Cloud computing? Location based services? Social networking? No can do, though you can still get into a raging debate about the relative merits of Macs and PCs. When it comes to federal privacy law, alas, we are running on code written in 1986: The Elecronic Communications Privacy Act, a statute that’s not only ludicrously out of date,... Cato-at-liberty blogs http://www.medworm.com/rss/comments.php?id=3424830 Wed, 31 Mar 2010 12:50:41 +0100 3424830 http://www.medworm.com/index.php?rid=3412550&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fl3o4RlKNgvU%2F I tend to agree with a lot of what Jeff Jonas has to say, but there are occasions I disagree. Jeff works for IBM, and in keeping with their Smarter Planet theme, he talks about real-time sensemaking systems and his beef with batch processing systems. He talks about it in this video The conclusion is that without real-time analysis you are going to be left behind. I will take the opposite view. In many cases, perhaps even the majority of cases, even if you were able to do real-time analysis, your response time would be so much longer, either out of necessity or just inability to respond, that it doesn’t really matter if the analysis is real-time, or deferred by a few hours or even days. I’ve always been a fan of just-in-time systems, i.e. a hierarchical set of systems where, fo... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3412550 Sat, 27 Mar 2010 22:10:22 +0100 3412550 http://www.medworm.com/index.php?rid=3408576&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FW0l0UZoo8Pg%2F Image by mndoci via Flickr In writing about potential shifts in the approaches to High Performance Computing, Andy Jones of NAG writes As a HPC community we lost control of much of our hardware to the commodity market some years ago. Maybe we now face losing control of our software to the commodity community too. In general, commoditization is a good thing, although there is always a place for purpose-built or specialized systems. The context of this piece was a panel where John West of InsideHPC talked about the commoditization of HPC software as the next big disruption after GPU Computing. John adds to some of those thoughts in his own post, essentially saying that as the general availability of parallel-capable hardware increases, the current HPC drivers will become a minority in t... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3408576 Fri, 26 Mar 2010 06:01:08 +0100 3408576 http://www.medworm.com/index.php?rid=3378672&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FuajzIgsb1Ek%2F For those curious about what gets my juices flowing these days and why I am fascinated by scale and my current job, just watch this talk (you will need Silverlight to view this, so apologize in advance). Warning: If servers and power utilization aren’t your thing, you might be in trouble. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3378672 Thu, 18 Mar 2010 02:10:21 +0100 3378672 http://www.medworm.com/index.php?rid=3374317&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fc1De80F8vSM%2F In a brilliant piece entitled Big Data Is Less About Size, And More About Freedom, Bradford Cross talks about about the democratization of analyzing data at scale. As he so correctly points out, the data age has a lot to do with the cool things we can do with data today. Yes data sizes are getting large, but large is relative. I heard numbers today that make the output from many genomics centers sound like a walk in the park, but for the average lab, the average startup, increasing amounts of data are still only in the range of terabytes, not petabytes as some of us (like yours truly) like to talk about. Brad talks about trends in computing and software that have allowed data-driven companies like Flightcaster to get to market faster. He breaks down these trends into three chunks Storing ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3374317 Wed, 17 Mar 2010 12:00:40 +0100 3374317 http://www.medworm.com/index.php?rid=3374200&cid=t_348399_109_f&fid=38950&url=http%3A%2F%2Fwww.shockmd.com%2F2010%2F03%2F17%2Fcloud-computing-explained%2F Google published three videos to explain the main principles behind its three core businesses: search, ads and apps. This one is about the apps and explains the advantages of cloud computing. Beware cloud computing also has some downsides such as being unable to access data when the server is down, also security issues are always a threat, so take care. No related posts. 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=3374200 Wed, 17 Mar 2010 07:24:32 +0100 3374200 http://www.medworm.com/index.php?rid=3374318&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FvSimV7oadlg%2F Jesse Robbins gave what looks like a great presentation at a cloud event recently about the value of being prepared for disaster. In a world of warehouse-scale computing an operational mindset is critical to success. What does it really mean? One way of looking at it is thinking about operational software, i.e. about software that understands that failure happens unexpectedly. Yes, this is something you can’t avoid at scale, but even at smaller scales having software that can be reliable deployed in a world where things break is essential. For more, just check out Jesse’s presentation Cloud Operations Bootcamp: Culture View more presentations from Jesse Robbins. On a related note, check out this talk by Paul Borrill on Rethinking time in distributed systems (slides and abstra... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3374318 Wed, 17 Mar 2010 04:17:05 +0100 3374318 http://www.medworm.com/index.php?rid=3374210&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F03%2F16%2Fgoogle-public-data-explorer-for-healthcare%2F Google recently released its public data explorer which combines the Google visualization tools with public datasets include population data and health data. For healthcare, the initial launch includes Sexually Transmitted Diseases in the U.S. and Cancer cases in the U.S. The charts allow selection by state and time options. For these two charts, CDC data sources are used. So could this data explorer be used more broadly with other health data sets. For starters, those at Data.gov (although most of the health data sets are Medicare cost data). But could major disease registries open themselves up to this API so that medical researchers could visualize more data sources and generate more research questions more quickly.  This could be one solution for the for the lethal lag time.  The CDC... eHealth blogs http://www.medworm.com/rss/comments.php?id=3374210 Wed, 17 Mar 2010 02:42:20 +0100 3374210 http://www.medworm.com/index.php?rid=3370603&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FTkV3ISv4aFk%2F Times change. Last week I was at a local science event and the speaker talked about their data being in Seattle and their compute literally being diagonally across the country in Florida (something that sort of happened for various reasons). That is quite the distance for data to travel. It’s even more for a lot of data to travel. As I commented when asked about solutions to that problem, my answer was “don’t move the data”. Well it’s true. Even with companies out there that help you move large quantities if data, the only good solution for data at this scale is to keep the data in one place and move the compute around. Cheaper, more efficient, and a better use of the network. IMO, the days of moving data sets over the wire are long gone. You can move slices a... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3370603 Tue, 16 Mar 2010 12:00:35 +0100 3370603 http://www.medworm.com/index.php?rid=3363700&cid=t_348399_109_f&fid=38950&url=http%3A%2F%2Fwww.shockmd.com%2F2010%2F03%2F14%2Fcloud-computing-explained%2F Google published three videos to explain the main principles behind its three core businesses: search, ads and apps. This one is about the apps and explains the advantages of cloud computing. Beware cloud computing also has some downsides such as being unable to access data when the server is down, also security issues are always near you so take care. No related posts. 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=3363700 Sun, 14 Mar 2010 16:24:32 +0100 3363700 http://www.medworm.com/index.php?rid=3327067&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fdispatch-himss Every year, I describe my top 10 impressions from HIMSS. Here's my summary of the event for 2010: 1. Meaningful Use is everywhere. Vendors are promising EHRs, modules, appliances, and services to help clinicians achieve it. I had dinner on Monday night in a small Indian vegetarian restaurant. Sitting next to me were 3 engineers from Bangalore who were arguing about the details of Meaningful Use in between bites of vegetable curry. I could not escape Meaningful Use anywhere! (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3327067 Wed, 03 Mar 2010 14:11:17 +0100 3327067 http://www.medworm.com/index.php?rid=3316144&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F02%2F27%2Fbook-review-googled-the-end-of-the-world-as-we-know-it%2F I recently completed this book by Ken Auletta who promotes his unique access to the search engine giant. The books follow the history of Google from the earliest days of the founders at Stanford, to rocketing to fame, going public and then being labeled as the evil empire. More recently, he chronicles conflicts with the government, traditional media, traditional advertising, publishers and China. He leaves with Google at a crossroads of maturing founders which he suggests may be losing focus, competitors in social media, and ongoing challenges from Microsoft and others. The book describes each new major app and the process and culture of building new tools and keeping them free. Only two pages are devoted to Google Health, however. Generally, the books focuses much more on the advertising ... eHealth blogs http://www.medworm.com/rss/comments.php?id=3316144 Sun, 28 Feb 2010 02:44:11 +0100 3316144 http://www.medworm.com/index.php?rid=3298425&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Ftop-5-dos-donts-speaking-analysts-himss The big health IT industry confab HIMSS kicks off one week from today. With some 28 briefings scheduled over 2.5 days, the Chilmark Research team will be extremely busy to say the least. It is with that in mind that Chilmark has prepared the top 5 dos and don’ts that all vendors need to keep in mind when briefing analysts to insure that these briefings are fruitful for both parties. (This post is as much for self-preservation as it is a public service.) (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3298425 Tue, 23 Feb 2010 13:26:25 +0100 3298425 http://www.medworm.com/index.php?rid=3275912&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fdata-lockers-healthcare Online data lockers are barely a ripple in the IT pond, showing up as secure sites where individuals can keep Web site passwords and other information, or as basic computer backup services. But as consumer data becomes more important to businesses, and cloud computing ditches the need for physical presences, this technology may very well put customer data in the hands of consumers - even in healthcare. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3275912 Tue, 16 Feb 2010 14:13:48 +0100 3275912 http://www.medworm.com/index.php?rid=3248663&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FTvnl_7QU6hU%2F I’ve written about the distributed self and science data platforms. A lot of the former was around the notion of pubsub, and pushing data to various places. Now imagine a scenario where you are using data from a variety of scientific repositories and you’ve built applications that use APIs to collect data. What if your data sources would update you everytime there was a change, so that your systems could automatically fetch any updates and rebuild anything that needed to be rebuilt, do any pre-computing that needed to be done. The model that Anil Dash talked about in his classic Push-Button Web post is relevant here as well. We have the tools to do this today. Real time, asynchronous messaging is part of distributed computing, and the variety of data repositories out there sho... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3248663 Sat, 06 Feb 2010 23:05:03 +0100 3248663 http://www.medworm.com/index.php?rid=3239750&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F__bk0ve1EoE%2F An Introduction to JavaScript Map/Reduce in Riak from Basho Technologies on Vimeo. Riak is a non-relational datastore with a cool API and nifty Map/Reduce features. The new features in version 0.8 are described here (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3239750 Thu, 04 Feb 2010 04:09:22 +0100 3239750 http://www.medworm.com/index.php?rid=3239533&cid=t_348399_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F006922.html What you can not hear is the massive silent sucking sound of Western corporate secrets flowing into servers in China. “The scope of this is much larger than anybody has every conveyed,” says Kevin Mandia, CEO and president of Virginia-based computer security and forensic firm Mandiant. “There [are] not 50 companies compromised. There are thousands of companies compromised. Actively, right now.” Mandia claims these intrusions are persistent and used for industrial espionage on a massive scale. Called Advanced Persistent Threats (APT), the attacks are distinctive in the kinds of data the attackers target, and they are rarely detected by antivirus and intrusion programs. What’s more, the intrusions grab a foothold into a company’s network, sometimes for years, even after a... (Source: F... FuturePundit blogs http://www.medworm.com/rss/comments.php?id=3239533 Thu, 04 Feb 2010 00:00:00 +0100 3239533 http://www.medworm.com/index.php?rid=3231638&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fblog-top-10-barriers-ehr-implementation Last week I taught Module II of Leadership Strategies for Information Technology in Healthcare at the Harvard School of Public Health. My students included administrators, clinicians, CIOs, CMOs, and policymakers. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3231638 Tue, 02 Feb 2010 13:48:36 +0100 3231638 http://www.medworm.com/index.php?rid=3223319&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2FtdELvXwT8qA%2Fgoogle_chrome_on_opensuse_112.php I decided to try using Google Chrome as a web browser. The reason is that it is supposed to be faster, particularly for sites that make heavy use of Flash. It turns out that installing it is a hassle if you do it the obvious way, because Flash does not work without fiddling around. That sort of defeats the purpose. The easier way is to use the one-click install at: http://software.opensuse.org/ymp/ope...2/chromium.ymp. This adds the necessary repositories, downloads the application, and configures it so that flash works right away. It seems to work pretty well. It remains to be seen, however, if Chrome has any chance of becoming my main browser. After all, the first browser I used was NCSA Mosaic, which morphed into Netscape Navigator, which went through several iterations, then becam... The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=3223319 Sat, 30 Jan 2010 12:31:27 +0100 3223319 http://www.medworm.com/index.php?rid=3220681&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fy-1PxDQWyFg%2F Software engineers on the team must equally understand that the code is just part of the science, and not usually a goal in its own right. That’s from an article titled Are we taking supercomputing code seriously? by Andrew Jones from the Numerical Algorithms Group Does that mean that code doesn’t have to be published after all? (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3220681 Fri, 29 Jan 2010 03:22:49 +0100 3220681 http://www.medworm.com/index.php?rid=3178941&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F15%2Fwhat-i-learned-this-week-about-productivity-mongodb-and-nginx%2F Productivity It was an excellent week. It was also a week in which I payed much less attention than usual to Twitter and FriendFeed. Something to think about… MongoDB I’m now using MongoDB so frequently that I’d like the database server to start up on boot and stay running. There are 2 init scripts for Debian/Ubuntu in this Google Groups thread. I followed the instructions in the second post, with minor modifications to the script: # I like to keep mongodb in /opt PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/opt/mongodb/bin DAEMON=/opt/mongodb/bin/mongod # you don't need 'run' in these options DAEMON_OPTS='--dbpath /data/db' # I prefer lower-case name for the PID file NAME=mongodb # I think /data/db should be owned by the mongodb user sudo chown -R ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3178941 Fri, 15 Jan 2010 08:45:46 +0100 3178941 http://www.medworm.com/index.php?rid=3163977&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FhPNIq8hQG5Q%2F I have written about TrendingTopics before. Pete Skomoroch gave a talk on how to build a data intensive web app using Hadoop, Hive and Amazon EC2 at Hadoopworld and the video is now available Building Data Intensive Apps with Hadoop and EC2 from Cloudera on Vimeo. Please see this disclaimer (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3163977 Tue, 12 Jan 2010 02:52:56 +0100 3163977 http://www.medworm.com/index.php?rid=3157623&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FYk77IaRONdw%2F In a recent editorial (sub might be required) talking about next-gen sequencing and cloud computing, Nature Biotech makes an all to familiar error. It remains unclear, however, whether the cost of routinely renting time on the cloud would be cost effective in the long term, particularly if a user intends to analyze billions of base pairs of genome sequence on a regular basis. What’s more, if the wide uptake of sequence analysis on clouds depends on the availability of user-friendly, debugged software, bioinformaticians might not be willing to spend the time to familiarize themselves with hadoop, the open source program needed to process large data sets on a cloud—especially when their jobs focus on developing algorithms for their own local computer clusters. The context for that... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3157623 Sat, 09 Jan 2010 17:09:35 +0100 3157623 http://www.medworm.com/index.php?rid=3153558&cid=t_348399_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=3139192&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fk_JinDgeKKo%2F Joe Landman has a series of posts providing a great perspective on HPC over the past decade. I suggest anyone interested in computing read them Part 1 Part 2 Part 3 – This one is a must read Part 4 Part 5 – Another great read and a subject that I used to blog about a lot (mostly channeling Joe) Part 6 – Close to home Part 7 – Storage technology, something I care about more and more (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3139192 Mon, 04 Jan 2010 15:42:00 +0100 3139192 http://www.medworm.com/index.php?rid=3133673&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2F2009-review-part-1 As I look back on 2009, it was a year of incredible change. I'll post this in two parts. The first includes Harvard Medical School and State/Federal work. The second will cover BIDMC. Harvard Medical School (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3133673 Wed, 30 Dec 2009 18:59:00 +0100 3133673 http://www.medworm.com/index.php?rid=3097005&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FIQslJKmQsNc%2F Greg Linden has a great article in Communications of the ACM on The Rise of the External Brain. As Greg notes, we have spent a lot of time trying to develop an Artificial Intelligence, a task at which we have not been successful. But he notes that we have had some success from in the form of chaos from the internet. The web, especially search engines supplement our own brain, filling in incomplete bits of knowledge when required. This viewpoint is in direct contradiction to the kinds expressed by Nick Carr, who believes that search engines are not a positive influences on our intelligence. I find myself aligning with Greg. He writes And so it is fitting that the biggest progress on building an external brain also comes from chaos. Search engines pick out the gems in a democratic sea of c... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3097005 Thu, 17 Dec 2009 07:51:18 +0100 3097005 http://www.medworm.com/index.php?rid=3079379&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2FjVUIm0YBzfc%2Ftech_tip_8.php This is a tip for selecting the fastest DNS server.  OpenDNS already has fans at ScienceBlogs (1 2).  I've been using it for years.  But now that Google has their own free/open DNS service, the question arises: which is better?  Or is there a different one that is better?  OpenDNS is free for anyone to use, but they also offer paid services to enterprises.  Those enterprises have special needs, which most of you would not want.  Google is, well, Google.   The tip is this: you can download an application which will test various open dns servers, and tell you which is fastest, on average, for your particular setup.  As it happens, the program is hosted/sponsored by Google, so you might wonder if it is does a fair test.  Go head and wonder. &... The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=3079379 Fri, 11 Dec 2009 13:56:25 +0100 3079379 http://www.medworm.com/index.php?rid=3079512&cid=t_348399_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=3075615&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcloud-computing-security-and-privacy-considerations While conducting research for the long overdue and nearly completed report on Personal Health Clouds (Dossia, Google Health and HealthVault) came across a recently published report by the European Network and Information Security Agency (ENISA) addressing cloud computing security.  Though quite long (over 120 pages) the report provides a very comprehensive overview of cloud computing, its benefits, risks and some very good risk assessment tools to assist one in evaluating a cloud solution (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3075615 Thu, 10 Dec 2009 14:28:17 +0100 3075615 http://www.medworm.com/index.php?rid=3071263&cid=t_348399_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2009%2F12%2F08%2Fthe-application-and-management-of-personal-electronic-inform.html The First International Forum on the Application and Management of Personal Electronic Information, organized by the MIT SENSEable City Lab, gathered many stakeholders from multiple disciplines to share on the issues surrounding the application and management of personal electronic information: The goal of this forum is to explore the novel applications for electronic data and address the risks, concerns, and consumer opinions associated with the use of this data. In addition, it will include discussions on techniques and standards for both protecting and extracting value from this information from several points of view: what techniques and standards currently exist, and what are their strengths and limitations? What holistic approaches to protecting and extracting value from data would w... Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=3071263 Tue, 08 Dec 2009 22:11:14 +0100 3071263 http://www.medworm.com/index.php?rid=3059857&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F4-uZcFNKCJE%2F Image via Wikipedia In a post announcing the open sourcing of Crane (more on Crane later), Bradford Cross writes A big concern with the modern JVM languages like Scala and Clojure is the ability to scale out from the single JVM address space into distributed environments. Different approaches include a distributed JVM (terracotta), distributed actors (akka), message queues (AMQP/rabbitmq), or solutions for specific computational models, like hadoop He also writes For those of us who are researchers, all our jobs are ad hoc transient clusters, and the problem is even more pronounced unless we have a dedicated research cluster, for the cluster must be brought up and torn down for every job. Researchers become “babysitters” to clusters and jobs; the master serves the servant. I... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3059857 Fri, 04 Dec 2009 16:57:19 +0100 3059857 http://www.medworm.com/index.php?rid=3039956&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F11%2F30%2Fa-brief-survey-of-r-web-interfaces%2F 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 all and the third is broken. R-Online Or rather, not online. Unless this CGI form is the same thing. I tried Example 1, it returned a server error. Rcgi Links to several CGI forms, none of which worked for me. CGI-based R access Link did not load. CGIwithR Package now maintained at Omegahat. Did not attempt installation. Last updated 2005. Rpad I could not connect to this URL. RApache The pick of the bunch. Provides server-side access to R through an Ap... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3039956 Mon, 30 Nov 2009 03:03:39 +0100 3039956 http://www.medworm.com/index.php?rid=3029915&cid=t_348399_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2009%2F11%2F25%2Fthe-razionalizer.html Via Leeander The “Rationalizer”, is a new concept device by Philips that is designed for “mirroring" your emotions. The user wears an Emobracelet on his/her wrist which measures the arousal component of the user’s emotion through a galvanic skin response sensor. The EmoBracelet is wirelessly connected with the EmoBowl, a bowl with lighted patterns that displays user’s emotional status. The range is a soft yellow, orange, or deep red. When the user sees that the bowl is flashing red, it means that it might be good to take a breather and calm down before making any irrational decisions (i.e. risky investments). See how the Razionalizer works in this concept video:   (Source: Positive Technology Journal) Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=3029915 Wed, 25 Nov 2009 20:07:00 +0100 3029915 http://www.medworm.com/index.php?rid=3003977&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F11%2F18%2Fturn-emacs-into-an-ide%2F I fired up NetBeans at work today, tried to open a Rails project and – inexplicably, it crashed. All is well at home, so I’m blaming work machine setup issues as-yet unknown (but I suspect, involving the letters “ATI”). It got me thinking that, as much as I like NetBeans, it is still just a memory-eating, CPU-hogging, bloated Java-based GUI. For some time I’ve wanted to convert my favourite editor, Emacs, to something more like an IDE. It's Emacs, but not as we know it The WyeWorks Blog to the rescue. Install emacs-23 and a couple of Ruby gems, clone their github repository of Emacs plugins, copy to your ~/.emacs.d/ and voilà – marvel at your new, shiny editing environment. I also replaced my ~/.emacs with their init.el file. The key plugins include ECB... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3003977 Wed, 18 Nov 2009 03:47:32 +0100 3003977 http://www.medworm.com/index.php?rid=2967467&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F11%2F06%2Fr-has-a-json-package%2F Named rjson, appropriately. It’s quite basic just now, but contains methods for interconversion between R objects and JSON. Something like this: > library(rjson) > data <- list(a=1,b=2,c=3) > json <- toJSON(data) > json [1] "{\"a\":1,\"b\":2,\"c\":3}" > cat(json, file="data.json") Use cases? I wonder if RApache could be used to build an API that serves R data in JSON format? Posted in computing, R, statistics Tagged: cran, json, r-project, statistics (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2967467 Thu, 05 Nov 2009 23:44:44 +0100 2967467 http://www.medworm.com/index.php?rid=2963175&cid=t_348399_109_f&fid=38950&url=http%3A%2F%2Fwww.shockmd.com%2F2009%2F11%2F05%2Fgoogle-apps-tricks%2F If your like me, having 5 e-mail accounts, a couple of websites, wikis, several calendars and address books it’s hard to keep everything in sync. Cloud computing or living in the Cloud has it’s benefits. Cloud Computing refers to Internet-centric software and services that are outsourced to someone else and in this case to Google. Everything is on the servers of google and you can access it from anywhere with a browser when connected to the Internet. Advatages of cloud computing with Google: it’s free or cheap, for 50 dollars a year you get support back up up time of 99% platform and browser agnostic constant improvements someone els is responsible for the hardware reliability you can share your information. Google wave hasn’t replaced this for me yet. If you need some gu... Dr Shock MD PhD blogs http://www.medworm.com/rss/comments.php?id=2963175 Thu, 05 Nov 2009 07:42:22 +0100 2963175 http://www.medworm.com/index.php?rid=2950918&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F11%2F02%2Fbrief-notes-on-ubuntu-9-04-jaunty-9-10-karmic%2F Recording my Ubuntu upgrade experience has become something of a tradition, so here goes. Machine 1 (laptop, LG T1 Express Duo). Largely trouble-free. On-board soundcard not seen on reboot. Fixed (temporarily, lost on reboot) using “sudo alsa force-reload”. Machine 2 (various generic hardware, cobbled together over many years). Upgrade smooth until final restart, when machine froze. Rebooted to a blank screen. Fixed by swapping out ATI video card for old NVidia FX5200. Discovered that rsyslog is running riot due to a hot CPU and is trying to fill up /var/log. Machine 3 (Dell Optiplex GX550). Install froze at “stopping winbind server”. Rebooted with rescue CD, mounted and chroot-ed into Linux partition, tried “dpkg –force-all –configure -a”, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2950918 Mon, 02 Nov 2009 08:18:12 +0100 2950918 http://www.medworm.com/index.php?rid=3123425&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2009%2F10%2F29%2Fthinking-about-the-future%2F What will the Web Look Like in 5 years? Gartner presented Eric Schmidt, CEO of Google to talk about the future. Some of his key points include: Five years from now the internet will be dominated by Chinese-language content. Today’s teenagers are the model of how the web will work in five years – they jump from app to app to app seamlessly. Five years is a factor of ten in Moore’s Law, meaning that computers will be capable of far more by that time than they are today. He also talks about being trapped in a 1980s architecture. I heard a webinar demo of an app today which uses client-server technology. It seems to me that any application which does not use the web with AJAX and hosted on a virtual server is old technology and not something that should be supported. Schmid... eHealth blogs http://www.medworm.com/rss/comments.php?id=3123425 Thu, 29 Oct 2009 05:17:00 +0100 3123425 http://www.medworm.com/index.php?rid=2931183&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F1RZnbWDfqug%2F Software is really becoming the broader language of science. Even broader than mathematics, but we don’t really know how to fund it. Those are words from Ed Seidel, Director of the NSF’s Office of Cyberinfrastructure. They are included in an article at Inside HPC, where Ed tries to clear up the air on some controversial positions on the status of supercomputing software. Whether you agree with Ed Seidel on whether Fortran is antiquated or not, it’s pretty clear, and not just in HPC that science does not know how to fund sustainable software development, and if we do want to get a generation of programmers into scientific computing, we have to embrace more “modern” programming languages, or develop our own, because whether you like it or not, getting good Fortran p... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2931183 Tue, 27 Oct 2009 02:30:43 +0100 2931183 http://www.medworm.com/index.php?rid=2923225&cid=t_348399_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2009%2F10%2F23%2Ffriday-foolery-8-dynamic-laika-sputnik-and-pandoras-box%2F @fackeldeyfinds on Twitter alerted me to the following video saying: “This one is for you”. more about “LAIKA on Vimeo“, posted with vodpod Indeed the video is about Laika Sputnik, but not about me, nor Laika the dog, but about a dynamic font “that can seamlessly use the whole spectrum of its cuts. A font that is [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=2923225 Fri, 23 Oct 2009 11:36:28 +0100 2923225 http://www.medworm.com/index.php?rid=2836304&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FkYErcJwifaI%2F Image via Wikipedia Just read the transcript of what sounded like an excellent talk by Greg Pfister about the next 20 years of HPC. Here are some of the key points of his talk Computing will become cheaper, but not necessarily much faster per processor There will be democratization of at least some HPC. In other words with faster processors and accelerators, we might all have access to some sort of TeraFLOPS device Computing will be done all over the place, with a lot being done in the cloud. I am not quite sure I get what Greg was aiming at with his section on garbage computing, but my guess is that the cycles we’ll consume might not be the highest quality cycles but they’ll get the job done You will be billed by how much power and bandwidth your computation consumes, not ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2836304 Sun, 27 Sep 2009 03:24:36 +0100 2836304 http://www.medworm.com/index.php?rid=2820503&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJlkzuU7et6I%2F John West puts it best Iris. Indigo. Indy. Octane. O2. Crimson. All SGI machines that I had on (or under) my desk back when I used to do real work. They were the best graphics machines money could buy in the day and they are still strong brands today, decades after their introduction. Makes me all nostalgic. The machine can be configured with 80 Nehalem cores and is being positioned along similar lines as the Nvidia Tesla-based machines, i.e. as a "personal supercomputer" John has a lot more on the announcement, not all sweet and nostalgic Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2820503 Tue, 22 Sep 2009 01:51:32 +0100 2820503 http://www.medworm.com/index.php?rid=2809848&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FruD3vCSXd08%2F Over the next few months, I’ll be giving a bunch of talks about large scale data. I will be talking at Hadoop World about “Hadoop for Bioinformatics“, at a Cloud Computing for Hedge Funds and at Supercomputing. Thinking through what I want to cover at all these talks has my brain in overdrive these days. At the same time discussions with various people facing data-related challenged provides a reality check and reminds me that there is still a long way to go. The one concept that people need to start putting their head around is the relative location of compute and data. Many people still think along the “move data to the compute” paradigm. When our data sets were small, this was not a problem. As instruments provide more and more data, ever faster, that tends... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2809848 Sat, 19 Sep 2009 03:33:17 +0100 2809848 http://www.medworm.com/index.php?rid=2762089&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FLEO5gXFx4L0%2F Image via CrunchBase Disclaimer: Newbie post ahead One of the more fascinating aspects of Hadoop is speculative execution. In many bioinformatics setups, there is some logic written, which examines your available resources, especially if you are using Sun Grid Engine, LSF, etc, the size of your input and chunks up your data appropriately and makes that data available to various nodes for computing on that chunk. In most of the implementations that I am aware of, this is done using a shared filesystem, often an NFS server. More recently, cluster file systems have become more popular for their improved availability characteristics. But in most pipelines job completion is analyzed post-job and you re-run any failed job. When you have a few 100 GB’s of data and a few 100 jobs that don... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2762089 Wed, 02 Sep 2009 22:34:49 +0100 2762089 http://www.medworm.com/index.php?rid=2752089&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F09%2F01%2Ffix-kile-for-ubuntu-9-04%2F Ubuntu/jaunty rocks, on the whole. However, to prove that newer does not always equal better, they threw in a couple of shockers. The first is the upgrade from the excellent Amarok 1.4 to the completely-broken 2.0. Head here to repair the damage. Kile is by far my favourite LaTeX editor and suffered, though not as badly, in the upgrade from 2.0 to 2.1. Reports of various problems litter the web; in my case I see broken toolbar buttons that do nothing when clicked. This fix is much simpler. Just “sudo apt-get remove kile”, scroll to the bottom of the intrepid package page, choose your architecture, download the deb file and “sudo dpkg -i kile_2.0.1-1ubuntu1_i386.deb”. I had no dependency problems and it works just fine. Finally – open up Synaptic, find kile and... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2752089 Tue, 01 Sep 2009 08:36:48 +0100 2752089 http://www.medworm.com/index.php?rid=2741536&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FrTcaSctX1oc%2F At the Hot Chips conference there was a lot of discussion around the need for a killer app for multicore.  First, I hate the phrase "killer app".   Sounds like a marketing cliche in the world of engineering, but looking past that, I remember writing a blog post from a conference I attended in 2006 where Jack Dongarra talked about the problem being the software.  Unfortunately more than three years later, we still seem to be talking about the same things.  I am with Dan Reed.  Where are the abstractions?  Until this, this will remain a very niche space whether we like it or not. Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2741536 Thu, 27 Aug 2009 14:33:33 +0100 2741536 http://www.medworm.com/index.php?rid=2738006&cid=t_348399_150_f&fid=38374&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FePharmaSummit%2F%7E3%2F_y8W2oXd4KU%2Fis-web-20-past-its-hype-cycle-in-pharma_26.html (Source: ePharma Summit) ePharma Summit blogs http://www.medworm.com/rss/comments.php?id=2738006 Wed, 26 Aug 2009 20:40:00 +0100 2738006 http://www.medworm.com/index.php?rid=2734124&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2009%2F08%2F25%2Fcloud-computing-tops-gartners-list.aspx%3Fref%3Drss Gartner's Hype Cycle for Emerging Technologies includes an evaluation of cloud computing. They view cloud computing as being at the Peak of Inflated Expectations. While companies look to the cloud for cost effective solutions, "The levels of hype around cloud computing in the IT industry are deafening, with every vendor expounding its cloud strategy..." Another post on the Emerge Blog, sees cloud computing as a promise without hype noting three cloud based models: Infrastructure-as-a-Service (IaaS)Platform-as-a-Service (PaaS)Software-as-a-Service (SaaS)This is a helpful formulation especially since so many platforms are becoming available in the Cloud and specifically in health care: Google Health and Healthvault to mention just two. While there is still concern about security in cloud com... eHealth blogs http://www.medworm.com/rss/comments.php?id=2734124 Wed, 26 Aug 2009 10:10:43 +0100 2734124 http://www.medworm.com/index.php?rid=2730294&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F4PAYAQ9Q6YI%2F The industry expects processors with 64 cores or more will arrive by 2015, forcing the need for parallel software, said David Patterson of the Berkeley Parallel Lab. Although researchers have failed to create a useful parallel programming model in the past, he was upbeat that this time there is broad industry focus on solving the problem. – Source: EE Times That lack of a programming model is already a major issue.  Where is the equivalent of a Hadoop for multicore?  I’m not the only one who’s wondered that.  Or is it just a problem that’s too hard to solve Posted via email from Flashing Neurons!!! (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2730294 Mon, 24 Aug 2009 23:19:39 +0100 2730294 http://www.medworm.com/index.php?rid=2725178&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FnqTQ9kfFrOc%2F Artificial DNA nanostructures1, 2 show promise for the organization of functional materials3, 4 to create nanoelectronic5 or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands'6, can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technol... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2725178 Thu, 20 Aug 2009 00:17:37 +0100 2725178 http://www.medworm.com/index.php?rid=2716153&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FPg6jfGXeIWQ%2F Artificial DNA nanostructures1, 2 show promise for the organization of functional materials3, 4 to create nanoelectronic5 or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands'6, can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technol... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2716153 Thu, 20 Aug 2009 00:17:37 +0100 2716153 http://www.medworm.com/index.php?rid=2712294&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fqm-xYwthDJk%2F Over the years, I’ve written about the web as a connected entity, with nodes notifying other nodes of an event or action. At various times this has been called the “just in time” web and more recently, in a narrower context, the distributed self. However, it is only in the last several months that I have come to appreciate the inefficiencies of polling and the potential of an event-based, notifications oriented web architecture, and I do believe as we stream more and more scientific data, such architectures are only going to get more common in the sciences, or at least I hope they do. In a recent blog post about Smart Clients, Ilya Grigorik writes As more and more browsers start adopting HTML 5 features I’m hoping to see WebSockets become a reality within the next ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2712294 Wed, 19 Aug 2009 07:33:46 +0100 2712294 http://www.medworm.com/index.php?rid=2699692&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcloud-computing-right-health-it The announcement of Salesforce.com investing and coordinating development efforts with Practice Fusion has brought talk of “cloud computing” to the fore. Salesforce has been known as a leader in cloud computing, and moving healthcare IT to that “cloud” has raised questions by a number of observers. What, exactly, is “cloud computing?” Is it appropriate for health IT? What are the security issues and risks? (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=2699692 Thu, 13 Aug 2009 15:56:33 +0100 2699692 http://www.medworm.com/index.php?rid=2695454&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2009%2F08%2F13%2Fpublic-and-private-clouds--health-information-exchange-hie.aspx%3Fref%3Drss In healthcare, there has been hesitancy to consider cloud computing in spite of the promise of funding for electronic medical records and perhaps HIE.  The main issues in cloud computing and EMRs are security and availability. Security is governed by HIPAA including the upcoming regulations on data breaches. Security of EMRs and PHRs is also key in maintaining public trust in EMRs and by implication, medical practices. Availability is key as well as medical practices become dependent on real-time data from EMRs for medical decision making. Can the cloud provide the security and availability/reliabity for EMRs? Alternatively, are EMRs now becoming private clouds which can potentially interact with the public cloud, such as in the case of disease registries and public health initiatives... eHealth blogs http://www.medworm.com/rss/comments.php?id=2695454 Thu, 13 Aug 2009 09:03:37 +0100 2695454 http://www.medworm.com/index.php?rid=2674437&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F08%2F06%2Frsruby-in-the-irb-console%2F R is terrific, of course, for all your statistical needs. But those data structures! “Everything is a list.” Leading to such wondrous ways to access variables as “p <- Meta(gds)$platform", or "last <- mylist[[1]][length(mylist[[1]])]". Sometimes, you want something more familiar. An array, a hash, a hash of arrays. Or, you may need to access R data in the language of your choice – e.g. as part of a Rails project. In Ruby, IRB is your friend. On the right, an IRB session in which we invoke RSRuby, load the GEOquery library from Bioconductor, fetch a dataset from the GEO database and examine the metadata that describes the experiment. Result: a ruby hash of arrays, where the keys are covariate types (”sample, disease.state, description&#8221... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2674437 Thu, 06 Aug 2009 06:36:52 +0100 2674437 http://www.medworm.com/index.php?rid=2667623&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fhw9q25p_DmU%2F I have written previously about Trendingtopics.org as a reference site for data analytics using Hadoop and Hive. Pete Skomoroch, who developed the site has written a great follow up article on the Cloudera blog that anyone in the scientific informatics space needs to read. Those same people need to read Chapter 5 in Beautiful Data. There Jeff Hammerbacher writes about the role of the Data Scientist at Facebook. So why should people in the scientific community read those two resources? Big Data is now a fact of life, both in science and otherwise. Our systems, both from the infrastructure and computation standpoint were written for data sets of different sizes. At the same time we are moving towards a world where the need to combine data resources is becoming even more necessary than in the... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2667623 Mon, 03 Aug 2009 23:28:57 +0100 2667623 http://www.medworm.com/index.php?rid=2657838&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FzxgAjC8LQCY%2F Image via Wikipedia Dan Reed has written a lot of interesting posts/essays lately, many of which have been covered here. He comes from a world where compute horsepower is king, admittedly a world I cared about for a long time, and still do to this day. But many of us today live in a different world, where the focus on computing isn’t high performance, but data intensive. So it’s interesting when in a recent blog post, Dan writes One of the major lessons from web search and cloud data centers is the power of truly massive scale, near real-time data analysis. When anyone with a cheap cell phone and a web browser can extract data and insights from a non-trivial fraction of the human knowledge base, behavior and culture are transformed. I would like to believe that we can bring ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2657838 Fri, 31 Jul 2009 05:12:23 +0100 2657838 http://www.medworm.com/index.php?rid=2653944&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F30%2Fhow-to-combinations-of-covariates-using-ruby%2F I work with people who generate a lot of microarray data. One question that they often ask is: can we find those genes with a two-fold or more change in median expression under two or more different conditions? For example, let’s say that we have 3 conditions: “normal”, “adenoma” and “cancer”. That gives us 3 pairwise comparisons: normal-adenoma, normal-cancer and adenoma-cancer. Here’s a Ruby solution to the problem. First, I installed StatArray, a Ruby gem that provides statistical methods for array objects. It’s not been updated for 3 years, but seems to work. require 'rubygems' require 'statarray' Next, credit to David Burger for posting this code solution for combinations in Ruby. You give it an array of ele... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2653944 Thu, 30 Jul 2009 07:08:38 +0100 2653944 http://www.medworm.com/index.php?rid=2649206&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FdkywvyChkEo%2F Big Data and the networked future of science; not only is that the title of my talk at Ignite Seattle 7 next week, but also was the working title of my talk at VA Tech. I strongly believe that the future of the life sciences will include not only large data sets, but the need to merge and co-analyze diverse data sources. The size and complexity of these projects and the skills required means we need to think about new ways of addressing these data volumes. These challenges are being recognized across the board. In a recent abstract from a paper on NetSolve/D, the authors (including Jack Dongarra) The persistent mood of exhilaration in the research community over exponential increases in the capacity of computational resources has been tempered recently by the realization that a torrential... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2649206 Wed, 29 Jul 2009 03:44:44 +0100 2649206 http://www.medworm.com/index.php?rid=2634592&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F24%2Frsruby-and-rails-revisited%2F A couple of months ago, I wrote a brief guide to displaying R plots in a Rails application using RSRuby. It worked at the time – really it did – but since then, I’ve encountered problems. One is that despite sending the plot output to a PNG file, R X11 windows started to pop up on loading the web page containing the plot. Another is the appearance of long error messages related to “stack smashing” on terminating Mongrel server. Fortunately, I read an excellent guide by Ana Nelson, R on Rails with RSRuby, which convinced me that I was doing things all wrong. So here is an amended version of my R + RSRuby + Rails “Hello World” application. We start as usual with “rails Plotter”. Next, I like to delete the public/index.html file and gener... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2634592 Fri, 24 Jul 2009 01:15:57 +0100 2634592 http://www.medworm.com/index.php?rid=2630315&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FhFJFPSuH1HQ%2F Been thinking a lot about data, not in the least cause I have to start thinking about my talk at Supercomputing. There have also been a number of recent meetings, podcasts, blog posts, etc that have me thinking about data, and managing data again. I won’t talk about the specifics from the meetings I’ve been in, but a lot of the discussion and thinking has been around large quantities of data, ranging from unstructured data to highly structured data and how we can analyze them more efficiently. The one thing I can talk about is this blog post describing the release of HadoopDB. HadoopDB is a new stack that combines PostgreSQL, Hadoop and Hive, essentially combining MapReduce with DBMS technologies, specifically targeted at the analytics crowd. I won’t talk about pluses and... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2630315 Thu, 23 Jul 2009 06:28:10 +0100 2630315 http://www.medworm.com/index.php?rid=2606052&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fdispatch-washington Today I was in Washington attending two important meetings - an Institute of Medicine gathering to discuss healthcare information exchange and the HIT Policy Committee Certification/Adoption Workgroup. The Institute of Medicine meeting brought together 30 experts from computer science, informatics, and the health information exchange community to discuss the applications of grid computing technologies to health information exchange. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=2606052 Wed, 15 Jul 2009 12:39:17 +0100 2606052 http://www.medworm.com/index.php?rid=2571048&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F03%2Fgreat-work-ismb-microblogging-team%2F Another year, another ISMB/ECCB meeting and – another great blogging effort. It’s all at the FriendFeed group: ISMB/ECCB Stockholm 2009, with outgoing links to individual blogs too. Thanks and congratulations to all involved for a great effort. Looking forward to the official write-up. Posted in bioinformatics, computing, meetings, web resources Tagged: friendfeed, iscb, ismb, microblogging (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2571048 Fri, 03 Jul 2009 00:42:35 +0100 2571048 http://www.medworm.com/index.php?rid=2561491&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F07%2F01%2Fhow-to-search-across-linked-tables-using-acts_as_ferret%2F I’m in the process of adding search to a Rails application, using acts_as_ferret and ran into this issue. How to search a table using a field from another table, supplied by a foreign key? Let’s say you created a table for a model named Feature: create_table "features", :force => true do |t| t.integer "feature_name_id" t.integer "chromosome_id" t.integer "start" t.integer "end" t.string "strand" t.datetime "created_at" t.datetime "updated_at" end This model, Feature, belongs_to two models, FeatureName and Chromosome, each with a field “name”: create_table "feature_names", :force => true do |t| t.string "name" t.datetime "created... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2561491 Wed, 01 Jul 2009 07:38:40 +0100 2561491 http://www.medworm.com/index.php?rid=2553189&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F06%2F29%2Fat-a-complete-rails-loss%2F I’ve been banging my head against the wall for almost a week with a Rails application. This post is not a plea for help – I’d use a forum for that – just a record of the problem. That said, feel free to comment, especially if you have a similar problem. This is all using Rails 2.3.2, Mongrel 1.1.5, installed as gems on Ubuntu 9.04. The basic issue: 2 models, 2 controllers, 2 sets of views. Identical in almost every respect, little more than basic CRUD (index, create, update, destroy). (1) works, (2) does not. The details: 1. The models Model Organism: class Organism < ActiveRecord::Base has_many :chromosomes has_many :platforms validates_presence_of :name,:binomial,:taxid validates_numericality_of :taxid validates_uniqueness_of :name,:binomial,:taxid ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2553189 Mon, 29 Jun 2009 01:29:34 +0100 2553189 http://www.medworm.com/index.php?rid=2512436&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fn8F1gmyWjdQ%2F Image by vitroids via Flickr 100 nanoseconds a day. 100 nanoseconds a day. 100 nanoseconds a day That is amazing. I used to get supercomputing time to do 100 ns simulations during my PhD and those used to last days, but that’s exactly what NAMD has achieved recently. A recent review article by the folks at D.E. Shaw Research lays down the state of protein simulations. To put the 100 ns in context. That simulation was done on 300 cores. Given that you can get 1000 cores increasingly easily, that’s 1000 ns in 3.3. days assuming linear scaling. So when D.E. Shaw and co write that microsecond simulations are getting practical (increasingly feasible would be a better statement), they’re not just saying that. I think if access to 3000 cores and these compute scales becomes ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2512436 Mon, 15 Jun 2009 06:49:30 +0100 2512436 http://www.medworm.com/index.php?rid=2512437&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F9FxigN-boEI%2F In a blog post last year James Hamilton wrote about workloads in large scale network file systems. In his summary about of study on the subject he writes Some of the important points that spring out for me: the percentage of random access is increasing; for those accesses that are sequential, the runs are longer; file sizes are increasing, data is getting colder; file lifetimes are increasing; and client usage has very high skew. Those patterns sound a lot like some of the patterns I have seen in the life sciences recently, especially as we have to handle increasingly larger data volumes, which have varying levels of access patterns and usage. Seeing some of the data challenges that people close to home have been seeing, esp significantly higher write to read ratios, which makes caching... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2512437 Sun, 14 Jun 2009 06:14:55 +0100 2512437 http://www.medworm.com/index.php?rid=2473897&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FajvsnJzwVfI%2F I have been invited to give a Masterworks talk on Data Challenges in Genomics for Supercomputing 09. I would like to dive into the details about the technical and scientific challenges of high throughput genomics, from microarrays to next gen sequencing and beyond and how we need to be manage these data more efficiently. While part of my talk will be about my day job, I want it to be informed by challenges we face today and will face tomorrow as a scientific community. So to try and capture many of these challenges and gather facts and information I have started a wiki page which I have made public. Please feel free to add to that page with ideas and topics that interest you. To do so, you will have to login as user sc09 and password computing. I request that you add your name to any major... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2473897 Sun, 14 Jun 2009 04:51:36 +0100 2473897 http://www.medworm.com/index.php?rid=2469824&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FWCFA7hOvCok%2F In episode 21 of Coast to Coast Bio (not yet released) I talk about Hive. For those who may not know, Hive is a data warehouse infrastructure built on top of Hadoop. One of the most recent Amazon Public Data Sets is a sample of Wikipedia page stat statistics by Peter Skomoroch. The full data set powers trendingtopics.org. What is TrendingTopics? This site was built by Data Wrangling to demonstrate how Hadoop can power a simple data driven website. The trend statistics and time series data that run the site are updated periodically by launching a temporary EC2 cluster running the Cloudera Hadoop Distribution. Our initial seed data includes the content of wikipedia and hourly article traffic logs from the wikipedia squid proxy collected by Domas Mituzas. Why do I like this so much? Apart fr... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2469824 Wed, 10 Jun 2009 14:50:32 +0100 2469824 http://www.medworm.com/index.php?rid=2469825&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FQaTDdTcj_UQ%2F I’ve written about software failures in the past. As I get a better understanding of scale and architectures and talk to others about some of the core design principles of systems at scale, e.g. Recover Oriented Computing (also see this talk by James Hamilton), I realize how little most of us in the life science world think about some of these design principles. Most people in this space do not run data centers, and usually have limited access to resources at massive scale. Yet, we are going towards a data intensive world, and a world in which we could, in princple, perform massive optimization problems. So the question to ask is, when will we start seeing some of these design patterns start becoming the norm rather than the expception for computing in the life sciences? When will we... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2469825 Wed, 10 Jun 2009 07:06:01 +0100 2469825 http://www.medworm.com/index.php?rid=2452769&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcompetition-hellohealth The media darling, Jay Parkinson and his company, HelloHealth, may have some competition.  While Jay and company are promoting the HelloHealth brand and its attraction to the media, young immortals and Health 2.0 groupies, a young pediatrician has developed her own take on the doc who does house calls. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=2452769 Wed, 03 Jun 2009 15:55:51 +0100 2452769 http://www.medworm.com/index.php?rid=2441895&cid=t_348399_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2009%2F05%2F27%2Fnew-book-on-pervasive-games.html New book on Pervasive Games: “Pervasive Games: Theory and Design - Experiences on the Boundary between Life and Play ” by Markus Montola, Jaakko Stenros and Annika Waer (editors) published by Morgan Kauffman “Quickly emerging from the fast-paced growth of mobile communications and wireless technologies, pervasive games provide a worldwide network of potential play spaces. Now games can be designed to be played in public spaces like streets, conferences, museums and other non-traditional game venues – and game designers need to understand the world as a medium—both its challenges and its advantages. This book shows how to change the face of play—who plays, when and where they play and what that play means to all involved. The authors explore aspects of pervasive games th... Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=2441895 Wed, 27 May 2009 15:54:06 +0100 2441895 http://www.medworm.com/index.php?rid=2442321&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F05%2F27%2Fquerying-ncbi-entrez-database-fields-using-ruby%2F Here’s a problem. You’d like to construct a complex query at NCBI Entrez using various fields. Example: “9606″[Taxonomy ID] to limit your search to Homo sapiens. Except – you don’t know which fields are available for the database that you want to query. EInfo can return an XML file with this information. Ruby + Hpricot eats XML for breakfast. Here’s an example using the GEO Datasets (gds) database. #!/usr/bin/ruby require 'rubygems' require 'hpricot' require 'open-uri' doc = Hpricot(open("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gds")) (doc/'//fieldlist/field').each do |f| puts "#{(f/'/name').inner_html},#{(f/'/fullname').inner_html},#{(f/'descr... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2442321 Wed, 27 May 2009 07:33:41 +0100 2442321 http://www.medworm.com/index.php?rid=2442320&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FMdHk3k0ZA8s%2F I recently heard someone talk about software as being operational. The context was large scale systems and how it is important not just to run hardware systems that operate at scale but also software that operates at scale. And having spent a lot of time lately in a world where operational excellence is paramount as well as the Hadoop world, the importance of operational software is becoming only more evident. As we work with very large data sets that need to be processed across 100’s, even 1000’s of commodity compute nodes, you need to run software that accepts and embraces failure. What makes the Hadoop framework work isn’t just the part that you can run map-reduce jobs, but the part where data is replicated in multiple locations, where the filesystem is distributed acr... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2442320 Mon, 25 May 2009 07:02:01 +0100 2442320 http://www.medworm.com/index.php?rid=2442902&cid=t_348399_158_f&fid=36018&url=http%3A%2F%2Fcaregiversbeacon.blogspot.com%2F2009%2F05%2F81-year-old-youtuber-over-5000-5-star.html Peter Zimmer, an 81 year old widower, of AskGeriatric.com has had over 2 million visitors to his youtube channel.He provides a huge variety of helpful information for senior citizens, as well as telling his life story on videos. Featured in many international magazines, such as Time Magazine, he is an incredible example of someone born during the "Paper Generation" who has joined the "Online Generation." (Source: The Caregiver's Beacon - Resources, Links, Ideas, News) The Caregiver's Beacon - Resources, Links, Ideas, News blogs http://www.medworm.com/rss/comments.php?id=2442902 Sun, 24 May 2009 20:55:00 +0100 2442902 http://www.medworm.com/index.php?rid=2424370&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F05%2F20%2Fbaby-steps-with-rsruby-in-rails%2F Plotting and charting libraries for Ruby (on Rails) abound. However, few are sophisticated enough for scientists and many are not actively maintained. Plotting in R, on the other hand, is about as sophisticated as it comes. Can we bridge Ruby and R? Yes we can, thanks to Alex Gutteridge’s RSRuby. The next logical question: how to plot data using RSRuby in your shiny new Rails application? First, thanks to Peter Lane over at Ruby for Scientific Research, a relatively-new blog with some excellent introductory RSRuby articles. Thanks also to Alex for providing RSRuby. Install RSRuby My OS is Ubuntu 9.04 with rubygems 1.3.3, installed from source and Rails 2.3.2. This works for me: sudo gem install rsruby --with-R-home=/usr/lib/R --with-R-include=/usr/share/R/include Make the RSRuby... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2424370 Wed, 20 May 2009 10:27:04 +0100 2424370 http://www.medworm.com/index.php?rid=2399061&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FCUYIwqVu8O8%2F Image via Wikipedia Dan Reed has a great essay up on the Blog@CACM site about High Performance Computing and abstractions. He writes I am confident that high-performance computing can and should learn a few tricks from the world of web services. We need a Ruby on Rails External Link for defining parallel application frameworks and an Erlang External Link for concurrent specification. We need to focus on high-productivity computing, balancing human and machine performance. He is talking about the need for higher level abstractions in a world where message passing remains king, and having played with some MPI programming, it’s non-trivial and I would never ever dream of become an expert in parallel programming. According to Dan, the lack of higher level abstractions in the HPC spac... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2399061 Sat, 09 May 2009 16:27:47 +0100 2399061 http://www.medworm.com/index.php?rid=2380892&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2F71O7pYk2Cec%2Ftech_tip_7_-_reporting_malicio.php If you encounter a web site that contains malware (virus, trojan, etc.), how do you report it?  I had a devil of a time finding out.  A friend had forwarded a suspicious email to me.  The email contained a link.  The link indicated that it would take you to a text file that explained a finding about a chance of an asteroid hitting the Earth next year.  the file ended with .txt.exe, obviously a bad thing.  So I downloaded it, using Linux, of course (the .exe would not be able to do anything without me affirming that the file was to be opened with WINE, which I did not plan on doing).  I scanned it.  It was a backdoor trojan.  I searched for reports about the malicious site that was hosting the file, but there were no reports.  I located th... The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=2380892 Thu, 30 Apr 2009 15:28:13 +0100 2380892 http://www.medworm.com/index.php?rid=2376312&cid=t_348399_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2009%2F04%2F29%2Femotional-cartography.html Via Info Aesthetic The free-downloadable book Emotional Cartography - Technologies of the Self is a collection of essays that explores the political, social and cultural implications of visualizing intimate biometric data and emotional experiences using technology. The theme of this collection of essays is to investigate the apparent desire for technologies to map emotion, using a variety of different approaches.   (Source: Positive Technology Journal) Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=2376312 Wed, 29 Apr 2009 16:11:00 +0100 2376312 http://www.medworm.com/index.php?rid=2376542&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F6Tl4dmkhru4%2F This is an exciting time to be a data geek. Today, there was a webcast (which I missed) for Wolfram|Alpha, which I am super excited about and hope that it is as good as it could be. Google just launched a new feature that makes it easy to find and compare public data (some feel this was meant to upstage the Wolfram preview). The cool part about the Google announcement is that this is the first time they have made good use of Trendalyzer, the technology they acquired from Hans Rosling and company at Gapminder. I have already blogged about Talis Connected Commons and in recent days, Amazon Public Data Sets have added a number of new data sets, including all the NCBI Flu data and, a particular favorite, the University of Florida Sparse Matrix Collection. Update: We have Wolfram|Alpha video D... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2376542 Wed, 29 Apr 2009 03:36:24 +0100 2376542 http://www.medworm.com/index.php?rid=2376297&cid=t_348399_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fpoint-point-interoperability-and-persistent-document-exchange   In a recent letter to the HITSP panel describing the interoperability needed for meaningful use, I discussed point to point interoperability and persistent document exchange. Here are a few additional details about these approaches. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=2376297 Tue, 28 Apr 2009 13:58:59 +0100 2376297 http://www.medworm.com/index.php?rid=2349284&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FGS_LscZ1E5A%2F Image via Wikipedia As readers of bbgm know, one of the subjects that interests me the most is computing, even though I am hardly a guru, but I’ve been around long enough and close enough to the world of computing to notice and observe various trends in this space. Perhaps the most recent trend, and it appears a new phrase in the computing lexicon is data intensive computing, something that life scientists should be very cognizant of today, as I talk about in Science Big, Science Connected. This interest in data intensive computing and recent exposure to data centers and large scale operations has led me to pay even more attention to some blogs I’ve been following for a while. Specifically, two blogs that I read religiously are those of James Hamilton and Dan Reed. James write... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2349284 Mon, 13 Apr 2009 04:49:27 +0100 2349284 http://www.medworm.com/index.php?rid=2260175&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F_NWQxmFu708%2F I didn’t quite get Wolfram|Alpha when Stephen Wolfram wrote about it. Nova Spivack has a long article about Wolfram|Alpha following a demo that sheds a lot more light. In a nutshell, Wolfram|Alpha is not a search engine, nor a knowledge base, but a system that computes the responses to natural language questions. As I understand it, there are basic building blocks which will use used to compute responses. It would also appear that the goal is to answer questions around formal knowledge, in other words there is probably a lot of pre-computing that will have to happen behind the scenes. Now, you, me and everyone else on the planet is skeptical. Wolfram is mad smart, but NKS, which forms part of the basis for Wolfram|Alpha, wasn’t exactly a resounding success, but this particular ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2260175 Sun, 08 Mar 2009 06:52:21 +0100 2260175 http://www.medworm.com/index.php?rid=2190637&cid=t_348399_113_f&fid=34933&url=http%3A%2F%2Fpalmdoc.net%2F%3Fp%3D2207 It seems PalmOS is officially dead. The Palm Centro will be the last device produced by Palm to run on Garnet (PalmOS version 5.x) so says Ed Colligan recently. The future is WebOS and this is what the latest PDA phone from Palm, the Palm Pre, will run on. One of the Palm Pre’s radical changes is the departure from traditional Desktop sync and the reliance on data sync over the “cloud”. This means syncing with data on Exchange as well as pulling data from services like Google and even getting contact information from Facebook etc. As someone who has been syncing only with Desktop PCs all this time, this is somewhat a major departure from what I am used to. I thought I might experiment a bit more with getting my PIM data synced using “cloud services”. Firstly a... The Palmdoc Chronicles blogs http://www.medworm.com/rss/comments.php?id=2190637 Mon, 16 Feb 2009 05:00:00 +0100 2190637 http://www.medworm.com/index.php?rid=2163540&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F02%2F06%2Fadd-friendfeed-comments-and-likes-to-wordpresscom-posts-using-ruby%2F The problem FriendFeed aggregates your blog posts from WordPress.com. Naturally, people prefer to comment on your post at FriendFeed - it’s quicker, easier and more fun. However, you would like to see an indication of this activity back at the original blog post. The solutions You could self-host your blog using software from WordPress.org. This allows you to install plugins such as FriendFeed comments. But you’re at WordPress.com because you don’t want to self-host, right? So you just have to live with the absence of useful plugins. My advice: don’t try discussing issues like this one in the WordPress.com forums unless you’re the kind of person who enjoys comment threads at YouTube. For intelligent, mature and constructive discussion go to FriendFeed of cours... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2163540 Fri, 06 Feb 2009 07:50:43 +0100 2163540 http://www.medworm.com/index.php?rid=2150752&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F02%2F02%2Fbrief-notes-on-export-from-friendfeed%2F During discussion of the ISMB 2008 room, Thomas asks: “Does FF really provide long-term archival?” Lars points out that it’s as permanent as anything else on the Web, Dorothea points out that FriendFeed offer no guarantees and Deepak discusses the FriendFeed API. Question: how useful is the FriendFeed API as a tool to, for example, archive a FriendFeed room? We can access the ISMB 2008 room via the API using a URL like this: curl “http://friendfeed.com/api/feed/room/ismb-2008?format=xml” > ismb.xml We can also retrieve items in other formats by substituting “xml” in the URL with one of: json, atom, rss. Note that where a FriendFeed post contains a “N more comments” link, those comments are actually present on the page and revealed... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2150752 Mon, 02 Feb 2009 02:01:45 +0100 2150752 http://www.medworm.com/index.php?rid=2149674&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FhgYFe7V_hqw%2F Thinking a lot about the role of computing and informatics in modern science. As I like reminding people, that while many put me in the “bioinformatics” category, my training is in molecular simulation. Which is why a post by Joe Landman on dynamical systems and climatology caught my eye, particularly the following quote HPC systems accord us virtual laboratories that allow us to create and probe state spaces that may be impossible to consider in an experimental sense otherwise. I love informatics as much as the next guy, but also believe that using theory and simulation to probe for problems which we cannot address in other ways, to understand systems. Neil’s post on Big Data reminded me that I’m as guilty as others of neglecting this very critical aspect of scienc... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2149674 Sat, 31 Jan 2009 20:57:35 +0100 2149674 http://www.medworm.com/index.php?rid=2100876&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F14%2Fwikification-thinking-in-public%2F Over the last 3 years, I’ve stored many small snippets of information in a set of Google Notebooks. Sample topics: notes for blog posts, programming skills that I’d like to learn and preliminary (or half-baked) ideas for research or software projects. I’ve learned that: Whilst Google Notebook is great for scraping information from web pages, it leaves a lot to be desired in terms of editing and presentation Ideas left in private notebooks quickly become dead ideas Yes you can publicise, tag and collaborate at a Google Notebook, but this doesn’t fit with my workflow - or that of many others, I suspect. So, I’ve taken as much of the material as I want to make public and dumped it on a wiki at Wikidot.com. By the way, if you’re looking for a free hosted w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2100876 Wed, 14 Jan 2009 03:42:06 +0100 2100876 http://www.medworm.com/index.php?rid=2095831&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F11%2Feasy-visualisation-of-database-schemas-using-sqlfairy%2F BioSQL schema Here’s a common problem solved: how to generate a pretty picture of your database schema. A Google search throws up all manner of home-brewed solutions using graphviz, perl scripts and so on. Or you can make life easier and simply install SQLFairy. Under Ubuntu: as simple as “sudo apt-get install sqlfairy”. Next, dump your database tables, e.g. for MySQL: mysqldump -u username -p -d mydatabase > mydatabase.sql Finally, for a PNG image of your schema: sqlt-graph -f MySQL -o mydatabase.png -t png mydatabase.sql Too easy. Example shown is the BioSQL schema. update: if your schema lacks explicit foreign keys, try the –natural-join options (man sqlt-graph, man sqlt-diagram) Posted in bioinformatics, computing, linux, research diary  &nbsp... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2095831 Sun, 11 Jan 2009 08:45:44 +0100 2095831 http://www.medworm.com/index.php?rid=2083948&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F07%2Ftext-to-fasta-and-other-delights-of-the-shell%2F One thing I’ve learned in my current job is that some familiarity with Linux tools for processing text files: awk, sed, grep, head/tail, cut/paste and so on, often provides a speedier solution than writing a script in (insert scripting language of choice here). I know this stuff is trivial to shell gurus, but I still get a little buzz out of it. A couple of real-life examples. Delimited text to fasta Your collaborator has developed “peptides on a chip” and sends you a text file describing said chip where column 1 = spot number, column 2 = peptide sequence: 1 ELDQGSLATSF 2 VDLAATPTDVR 3 TTNEEYLDLSQ 4 SSLDVYDGRFL 5 ALVHSYMTGRR Your analysis requires that the peptide sequences be in fasta format. Easy, using awk: awk '{print ">peptide" $1 "\n&qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2083948 Wed, 07 Jan 2009 03:02:42 +0100 2083948 http://www.medworm.com/index.php?rid=2035629&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2Fwp-content%2Fuploads%2F2008%2F12%2FWPSubversion.mp4 As many of bloggers are no doubt aware, a major update to Wordpress was release this week. I, like many others, eagerly upgraded my installation to take advantage o many new long-awaited features (particularly on the admin/management end). However for many, upgrading WP means downloading the latest .zip archive, unpacking on one’s local disk, then uploading the entire contents of the unpacked archive (see the irony here?) through an FTP client, wondering why so many micro-tiny files would take soooo long to transfer (it’s very straightforward, but that’s for another discussion). During this frustrating process, one’s WP installation can become instantly unstable, as files are being upgraded in place, a real-time mix of two different versions. Not good for a heavy-tr... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=2035629 Mon, 15 Dec 2008 00:14:29 +0100 2035629 http://www.medworm.com/index.php?rid=2026879&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F12%2F10%2Fthesis-reflections%2F All these people finishing their theses takes me back to my own Ph.D. thesis writing experience. Not that I recall much about it at all; rather like giving birth, the memory erases the excruciating pain and substitutes a kinder, gentler version. I took way too long to write up, for a variety of reasons, but a major factor can be summarised in one word: Microsoft. In those days I was running Windows 3.1 and Word 6 (I think), on 433 MHz PC with 8 MB - yes, megabytes, of memory. It crashed. A lot. In fact I could not save documents that contained embedded images, so my solution was to insert the image, draw lines around it to indicate its position, remove the image and save. Before printing I added each image back, removed the lines, printed the page then removed the image again. Insane! Eve... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2026879 Wed, 10 Dec 2008 06:03:51 +0100 2026879 http://www.medworm.com/index.php?rid=2027174&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F43SfC6q3lRE%2F One wouldn’t have been able to tell looking at the huge Supercomputing booth, but SGI has been struggling for years. The company, whose machines were the mainstay of computational science, especially life science back in the day, and got this blogger through grad school, might just be on its final legs. Today, they received a delisting notice from the Nasdaq. Now, this is not the first time they’ve been in trouble, having filed for Chapter 11 in the past following delisting from the NYSE, so it’s entirely possible they will come out of it, but with the economy the way it is, and no real market for what they offer, I am not so sure. If it is the beginning of the end, it will be the end of a proud company that was once the epitome of visualization technology and built some ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=2027174 Wed, 10 Dec 2008 05:57:53 +0100 2027174 http://www.medworm.com/index.php?rid=2021476&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2F2008%2F12%2F849 As I blogged on Friday, I wanted to have some stuff up this weekend of a video nature, but my video options are being very, very uncooperative. I have an OLD version of Final Cut on the Mac, but it has since been corrupted and can’t be used right now. Still, it’s a sledgehammer when many times a simple stapler will do. In this case, I have video of a shell session (like a DOS command line) showing how to use Subversion to upgrade Wordpress. I actually I have another unrelated video as well, but they have two things in common: they need their audio replaced with another audio track (recorded on a better mic). Now if it was a straight 1:1 audio swap, that’s trivial. But I do need the help of a video editor w/rudimentary capabilities to stretch out the video on a frame for a... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=2021476 Sun, 07 Dec 2008 15:33:25 +0100 2021476 http://www.medworm.com/index.php?rid=2685182&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2F2008%2F12%2F849 As I blogged on Friday, I wanted to have some stuff up this weekend of a video nature, but my video options are being very, very uncooperative. I have an OLD version of Final Cut on the Mac, but it has since been corrupted and can’t be used right now. Still, it’s a sledgehammer when many times a simple stapler will do. In this case, I have video of a shell session (like a DOS command line) showing how to use Subversion to upgrade Wordpress. I actually I have another unrelated video as well, but they have two things in common: they need their audio replaced with another audio track (recorded on a better mic). Now if it was a straight 1:1 audio swap, that’s trivial. But I do need the help of a video editor w/rudimentary capabilities to stretch out the video on a frame for a... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=2685182 Sun, 07 Dec 2008 13:58:50 +0100 2685182 http://www.medworm.com/index.php?rid=2017501&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F12%2F07%2Fwhat-i-learned-from-clay-shirky-about-science-online%2F The “science online” community has somehow compiled a required reading list (thanks John!), from which many ideas and quotes are mined. I recently finished reading an entry on the list: Here Comes Everybody, by Clay Shirky. I enjoyed the book - much of it was familiar to me, but it makes good use of specific examples to convey general principles. Of more interest to me is the application of these ideas to science online. Here’s what I think we can extrapolate from the book - and this is purely my personal interpretation. Most online science communities will fail Why? Answer: almost everything on the Web fails. However, there is so much activity that a few ideas succeed. Shirky uses the notion of “failure for free”; if you have an idea, it costs little or not... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2017501 Sun, 07 Dec 2008 09:26:08 +0100 2017501 http://www.medworm.com/index.php?rid=2018352&cid=t_348399_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F12%2Fpublic-data-sets-on-aws-amazon-web.html "AWS hopes to provide researchers across a variety of disciplines and industries with tools to enable more innovation, more quickly" [Public data on AWS]If you are interested in cloud computing and storage then you will be delighted that Amazon offers support to the science community. Though appreciated, do I think that the information provided for the data sets is very sparse, e.g. which conformer generation was used for the chemistry data sets? How exactly was the UGI dataset created?Anyway, this sounds similar to the computing and storage solution of Google, called MapReduce and GFS. I do not know enough about it to understand the technical differences between the frameworks of Amazon and Google, but both are used to work with tons of data. As announced by Amazon would users (or compan... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=2018352 Sat, 06 Dec 2008 16:43:00 +0100 2018352 http://www.medworm.com/index.php?rid=1996394&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FuapRyZXidyw%2F Some time ago I wrote about how more data does not necessarily mean you get slower, channeling Jeff Jonas’ analogy to jigsaw puzzles. He extends some of those thoughts in a recent post on how obervations are accumulated into context. As usual I find a lot of parallels with the practice of data driven science, specifically bioinformatics. We have an increasing number of fragments of data. Some day, perhaps enough to actually build a complete puzzle. In this latest post, Jeff talks about some of the decisions we need to make. Should we favor the false negative by having tight constraints on when we snap two pieces together? Should we permit a degree of uncertainty and potentially find connections which we might otherwise miss, essentially raising the false positive rate. Jeff argues in... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1996394 Sat, 29 Nov 2008 06:07:56 +0100 1996394 http://www.medworm.com/index.php?rid=1990651&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F11%2F27%2Fopenid-dont-provide-if-you-wont-accept%2F Once again, an interesting FriendFeed discussion has morphed into a thread on a wider issue: OpenID. OpenID is one of those brilliantly simple ideas that you’d imagine most people would applaud. A single “digital identity”, used for any website that requires a login, rather than creating multiple accounts, usernames and passwords for each site. Here’s the problem: many services allow you to use your account details as an OpenID at other sites, but they won’t accept credentials other than their own. For example, both my WordPress and GMail accounts are OpenIDs, but I can’t login to Google using nsaunders.wordpress.com. You might ask - why? Is it some sort of “brand loyalty” issue? When I sign up to Service X, is there a contract between us suc... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1990651 Thu, 27 Nov 2008 07:23:26 +0100 1990651 http://www.medworm.com/index.php?rid=1984952&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FRVPeqfA5E6s%2F I have covered D.E. Shaw in the past here at bbgm. I have always been fascinated by a research organization funded by someone who has money and is interested in science, without necessarily feeling the need to commercialize it, and by all accounts a person who is very intelligent. That D.E. Shaw research was represented at Supercomputing 08 was not surprising, but the topic of the talk was not what I expected. That it was one of the more fun talks at the conference made it that much better. Tiankai Tu (at least I think it was him) gave a talk about HiMach, a framework for the analysis of very long (millisecond scale) trajectories from molecular dynamics solutions. As most of you probably know, D.E. Shaw Research has been building a purpose-built computer, Anton, for millisecond scale molec... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1984952 Tue, 25 Nov 2008 04:47:11 +0100 1984952 http://www.medworm.com/index.php?rid=1968719&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F11%2F19%2Freproducibility-understandable-if-not-desirable%2F Greg Wilson once told me a statistic concerning the mean lifetime of research software reproducibility. That is, the time that elapses on average after which you cannot reproduce your own results using your own code, never mind anyone else’s. I forget the exact number but it was not high - a few months at best. Why does this happen, aside from obvious bad practices? Well, here’s a typical exchange in an academic research setting: Doctor X: Oh! I should have included the PDB header and diffraction resolution in my database table. Guess I’ll have to modify my parser. Doctor Y: No, don’t do that. I have those columns in one of my tables. I’ll just dump them out and you can import them in. Doctor X: Great, thanks! Six months later… Doctor X: Hey, I’m ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1968719 Wed, 19 Nov 2008 07:50:38 +0100 1968719 http://www.medworm.com/index.php?rid=1955191&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F11%2F13%2Fgood-software-data-and-your-brain%2F I recently asked the FriendFeed community about wiki usage and was struck by a comment from Allyson: I think we’re on our third incarnation of various bits of wiki software, and we’ve finally hit on the right software for both our wet lab and bioinformaticians By “the right software”, she means software that makes sense to the people who use it. When faced with several software alternatives, we often find there is one which for some reason, “makes sense” - it meshes naturally with the way our brains work. When you find a program that you like, it’s not only a joy to use but can enable understanding of data and processes that previously eluded you. In other words, good software doesn’t shield you from the fundamentals - it illuminates them. ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1955191 Thu, 13 Nov 2008 03:23:08 +0100 1955191 http://www.medworm.com/index.php?rid=1947274&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FugJtSUgvJsQ%2F I’ve always liked , especially the interface and the distributed service driven model. But this is nothing to do with that. They have an iPhone app I already use the Molecules app on the iPhone and recently saw someone launch a sequence alignment job on EC2 from an iphone. I think the day of using mobile devices as part of regular scientific workflows is not that far away. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1947274 Sat, 08 Nov 2008 21:03:26 +0100 1947274 http://www.medworm.com/index.php?rid=1940170&cid=t_348399_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fscuppering-the-program-pirates.html Professors the world over are worried about plagiarism: students simply lifting huge chunks from web pages and passing the thoughts and arguments off as their own. Then there are the Professors who steal from each other and publish their work in supposedly novel research papers and books and present it at conferences as original. This kind of plagiarism seems to be on the increase. No one know the true extent to which it is being undertaken, but a few high-profile cases have increased awareness in the academic community of the paper pirates who could scupper your research career plans with a few well-stolen words. It could be that a whole generation of students and unscrupulous Professors are creating an information black market. In the long-term, it is the students’ education, the r... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=1940170 Fri, 07 Nov 2008 02:00:19 +0100 1940170 http://www.medworm.com/index.php?rid=1938982&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F11%2F06%2Fdokuwiki-pubmed-and-ruby%2F I recently built a wiki for a research group using DokuWiki, one of my favourite wiki packages. As with many other wikis, developers have extended its functionality by writing plugins. Some of these are excellent, allowing users to generate lots of content with a minimum of syntax. For example, using the PubMed plugin, you type this: {{pubmed>long:15595725}} and the result is this: Which got me thinking. Assuming that you’ve searched PubMed and retrieved a bunch of references in XML format, how might you generate text in DokuWiki syntax, to paste into your wiki? Here’s the small parser that I wrote in ruby: #!/usr/bin/ruby require 'rubygems' require 'hpricot' h = {} d = Hpricot.XML(open('pubmed_result.xml')) (d/:PubmedArticle).each do |a|... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1938982 Thu, 06 Nov 2008 08:54:13 +0100 1938982 http://www.medworm.com/index.php?rid=1939003&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2008%2F11%2F05%2Fbuilding-100-in-the-cloud.aspx%3Fref%3Drss A new Web 2.0 company, Drop.io, has its infrastructure virtually through Amazon making it totally dependent on the Cloud for hosting. Are there pros and cons to this? They see mostly pros - highly available, meet unpredictable growth needs, limit startup expenses, treat storage like the commodity it is. They like the variable cost as a start up as opposed to fixed costs. Maybe there is a lesson for Health 2.0 startups here.Technorati: Cloud Computing (Source: eHealth) eHealth blogs http://www.medworm.com/rss/comments.php?id=1939003 Wed, 05 Nov 2008 17:10:04 +0100 1939003 http://www.medworm.com/index.php?rid=1933090&cid=t_348399_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2008%2F11%2F04%2Ftextual-emotion-recognition-and-visualization.html From InfoAesthetics a textual emotion recognition & visualization engine based on the concept of synesthesia , or in other words: "code that feels the words visually". the synesketch application is able to dynamically transfer the text into animated visual patterns. the emotional parameters are based on a WordNet-based lexicon of words with their general & specific emotional weights, for the emotion types happiness, sadness, fear, anger, disgust, surprise. the visualization is based on a generative painting system of imaginary colliding particles. colors & shapes of these patterns depend on the type and intensity of interpreted textual emotions. (Source: Positive Technology Journal) Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=1933090 Tue, 04 Nov 2008 21:02:14 +0100 1933090 http://www.medworm.com/index.php?rid=1933517&cid=t_348399_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fscience-of-spam.html Who hasn’t received a spam email with some kind of clause laying claim to compliance with the CAN-SPAM Act of 2003? They usually say something about the message being anything but spam. But, it quickly becomes obvious, if you actually waste the time to read the content, that it is a generic marketing message for some kind of herbal remedy for enhancing one or other, or two, parts of your body, making you money, or offering an ugly gold-plated watch at a knock-down price. Of course, the can-the-spam legislation was meant to squash spam forever, although by not making spam officially illegal across the globe, it did nothing of the sort. It was baloney, in a can. In fact, Petur Jonsson, the Professor of Economics and Chair of the Department of Finance, Economics, Entrepreneurship, and M... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=1933517 Mon, 03 Nov 2008 12:00:47 +0100 1933517 http://www.medworm.com/index.php?rid=1883278&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F10%2F17%2Fthe-three-phases-of-mysql-usage%2F As Mike keeps reminding me, getting your data into database tables is A Good Thing. Like many people, my database of choice is MySQL - largely because it was the first one that I tried and it works for me. However, I’m far from being an expert MySQL user. In fact, I’ve identified 3 stages in my use of MySQL over the years; see if you recognise yourself in any of them. The single table database Early in your MySQL career, you discover either “LOAD DATA INFILE” or the command-line tool “mysqlimport”. You realise that this is a quick and easy way to get all of those delimited text files straight into a database. Off you go, merrily importing everything on your hard drive into tables. At some stage, you begin to wonder whether listing the same identifier (... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1883278 Fri, 17 Oct 2008 04:55:33 +0100 1883278 http://www.medworm.com/index.php?rid=1905978&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FYLB7xTe3mTU%2F Image via WikipediaMy favorite source of hardware acceleration commentary returns to that subject. Joe asks My question now is, given the intent of Intel in this market, will Larrabee be able to get traction in the graphics world? And therefore, effectively displace nVidia (and to a lesser extent, AMD) as the accelerator king? IMO, if Intel nails the programmability issue, they can make a huge dent into nVidia’s leadership. It’s all about the programming at this stage Related articles by Zemanta Intel’s Larrabee Aims to Take on Nvidia and AMD (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1905978 Wed, 15 Oct 2008 02:21:12 +0100 1905978 http://www.medworm.com/index.php?rid=1875997&cid=t_348399_122_f&fid=34755&url=http%3A%2F%2Fneuropsychological.blogspot.com%2F2008%2F10%2Finternet-use-good-for-brain-circuitry.html From The BBC:Internet use 'good for the brain'Read the full article[snip]Lead researcher Professor Gary Small said: "The study results are encouraging, that emerging computerized technologies may have physiological effects and potential benefits for middle-aged and older adults."Internet searching engages complicated brain activity, which may help exercise and improve brain function."The latest study was based on 24 volunteers aged between 55 and 76. Half were experienced internet users, the rest were not.Each volunteer underwent a brain scan while performing web searches and book-reading tasks.Both types of task produced evidence of significant activity in regions of the brain controlling language, reading, memory and visual abilities.However, the web search task produced significant addi... BrainBlog blogs http://www.medworm.com/rss/comments.php?id=1875997 Tue, 14 Oct 2008 16:27:00 +0100 1875997 http://www.medworm.com/index.php?rid=1860018&cid=t_348399_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fmobile-internet-insecurities.html Most internet users will be unaware and unconcerned by the computer science and technology that underpins their daily web surfing, emails, chats, and Twitter updates. But, there are, of course, thousands of incredibly bright people working behind the scenes to make the internet work. One aspect of the backroom work that goes on, is the development of the software systems that carry the packets of information across the internet, whether that’s to open a web page in your browser, connect your net phone to a friend across the ocean, or trap spam on its way to your inbox. At the moment, the internet is mainly running on a system known as Internet Protocol version 4, or IPv4. Version 4 was first mooted in 1981, years before the Web was invented and certainly long before broadband, Youtub... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=1860018 Mon, 06 Oct 2008 12:00:41 +0100 1860018 http://www.medworm.com/index.php?rid=1833127&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F27%2Fit-would-be-too-easy-to-rant-and-rave-about-this%2F Zotero is a marvellous, active open-source project, providing a Firefox extension that captures and formats bibliographic information from web pages. Thomson Reuters describe themselves as “the world’s leading source of intelligent information for businesses and professionals.” Whatever. They specialise in closed-source, proprietary solutions which to my simple mind is at odds with a role as an information source. Via FriendFeed from Rafael Sidi’s blog, I learn that Thomson Reuters are suing George Mason University, developers of Zotero, for “violating its license agreement and destroying the EndNote customer base”. Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1833127 Sat, 27 Sep 2008 02:15:58 +0100 1833127 http://www.medworm.com/index.php?rid=1811273&cid=t_348399_122_f&fid=34755&url=http%3A%2F%2Fneuropsychological.blogspot.com%2F2008%2F09%2Fself-navigating-wheelchair.html From the website, MedGadget::A Wheelchair with Ears and Brainhttp://www.medgadget.com/archives/2008/09/a_wheelchair_with_ears_and_brain.html (Source: BrainBlog) BrainBlog blogs http://www.medworm.com/rss/comments.php?id=1811273 Fri, 19 Sep 2008 15:55:00 +0100 1811273 http://www.medworm.com/index.php?rid=1809696&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2008%2F09%2F19%2Fthe-intelligent-cloud--implications-for-health-and-medicine.aspx%3Fref%3Drss "The best way to predict the future is to invent it."This phrase describes the future of cloud computing and more specifically, information storage and retrieval. Predictions from Google:By 2019, parallel-processing computer clusters will be 50 to 100 times more powerful we'll also see a rush of new devices customized to particular applications, and more environmental sensors and actuators, all sending and receiving data via the cloud.computer systems will have greater opportunity to learn from the collective behavior of billions of humansResearchers across medical and scientific fields can access massive data sets and run analysis and pattern detection algorithms that aren't possible today.There are likely other implications for health care, such as, accessing the the cloud (or a secure a... eHealth blogs http://www.medworm.com/rss/comments.php?id=1809696 Fri, 19 Sep 2008 15:04:20 +0100 1809696 http://www.medworm.com/index.php?rid=1794363&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2008%2F09%2F15%2Fcloud-computing--is-availability-meaningless.aspx%3Fref%3Drss This article poses the question of whether the traditional measures of availability, five 9's, is outmoded. If the primary data sources like Google maps and others have significant reliability, do the applications themselves have reliable hosting and application stability to provide this kind of availability? Technorati: Cloud Computing (Source: eHealth) eHealth blogs http://www.medworm.com/rss/comments.php?id=1794363 Mon, 15 Sep 2008 21:32:20 +0100 1794363 http://www.medworm.com/index.php?rid=1788673&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2008%2F09%2F12%2Fpersonal-cloud.aspx%3Fref%3Drss This post on the concept of a personal cloud focuses on the integration of the iPhone, Google tools and the cloud. How about a personal cloud for managing health? In his presentation on Google Health at HIMSS in February, Eric Schmidt envisioned storing health information, including all the xrays taken this year in the  Cloud so that they would be accessible from anywhere. Interesting concept. First, Google Health should be available via the iPhone. Next, the clound should allow connection to your data and health information and tools from anywhere and on any device.Finally, the personal cloud must be secure.Also mentioned is an Mac program called Getting Things Done. Check out the Wikipedia entry.Technorati: Cloud Computing (Source: eHealth) eHealth blogs http://www.medworm.com/rss/comments.php?id=1788673 Fri, 12 Sep 2008 16:36:50 +0100 1788673 http://www.medworm.com/index.php?rid=1773166&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F08%2Fon-parsing%2F Parsing - the act of ripping through a file, pulling out the relevant parts and doing something useful with them, is an integral part of bioinformatics. It can be a dull procedure. It can also be challenging, requiring creativity and imagination. Frequently as a bioinformatician, you will generate output from an unfamiliar program, or a colleague will bring you a file that you haven’t encountered. Your task is to figure out how the file is structured, which regular expressions are required to parse it, what kind of output to produce and most importantly, how to handle those rogue files which don’t obey the rules. Here’s my top ten (language-agnostic) parsing tips, focusing only on unstructured (non-XML) text files. Search for an existing parser… Most of us don&#82... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1773166 Mon, 08 Sep 2008 06:09:44 +0100 1773166 http://www.medworm.com/index.php?rid=1750048&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F09%2F02%2Fdata-capture-versus-data-archiving%2F The commonest complaint that I hear whenever electronic lab notebooks (ELNs) or laboratory information management systems (LIMS) are discussed is that it doubles the workload. People who work in labs enjoy the convenience of their paper notebooks. They perform an action or a process occurs - they write a note. A machine generates a photo - they tear it off and paste it in. Transferring that information to a digital archive is a pain: they have to sit down at a computer with their lab book, scan and upload images, enter text into form fields and so on. I sympathise, absolutely. At present, data capture and data archiving are for most people, disconnected processes. Their only comfort is that smart people are working on these problems. One day, laboratory equipment will emit data in machine-... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1750048 Tue, 02 Sep 2008 02:31:24 +0100 1750048 http://www.medworm.com/index.php?rid=1739636&cid=t_348399_113_f&fid=36670&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmsdn%2Fhealthblog%2F%7E5%2F332117283%2FTransforming%2520Medical%2520Data%2520Into%2520Knowledge%2520for%2520Better%2520Health.wma If you want to go straight to the really sexy stuff, scroll toward the bottom of this entry and see the photos and video of Microsoft Surface in Health.  If you want a more complete view of the day's proceedings, read on. Yesterday ended with a very nice cocktail reception held at the Microsoft Conference Center; the site for our annual Microsoft Healthcare Users Group meeting in Redmond.  I always look forward to the social events around our conference as an opportunity to catch up with good friends and business associates from around the country and the world. Turning Health Data into Knowledge Today kicked off with an opening keynote by Steve Shihadeh (left in the photo) VP of Sales and Marketing for our Health Solutions Group.  Steve spoke on "The Transformative Power of... HealthBlog blogs http://www.medworm.com/rss/comments.php?id=1739636 Wed, 27 Aug 2008 20:49:00 +0100 1739636 http://www.medworm.com/index.php?rid=1726316&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F08%2F23%2Fwhat-if-journal-current-contents-were-tag-clouds%2F In conclusion The best RSS summaries from journals contain abstracts Cluttering up your feed with section headers (often longer than the article titles) reduces readability and information content; I’m looking at you JBC and Science Pretty pictures in feeds contribute nothing (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1726316 Sat, 23 Aug 2008 10:11:17 +0100 1726316 http://www.medworm.com/index.php?rid=1711726&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F08%2F18%2Fmysteries-of-ccp4%2F Since moving to a structural biology group, I’ve had to become somewhat familiar with CCP4, a suite of programs that do all manner of things using structural data, typically PDB files. Being a bioinformatician, I tend to ignore the GUI in favour of the input -> script -> output approach, as I’m mostly interested in batch processing. Documentation describing this operation for CCP4 programs is strangely lacking on the web. The best that I can find is the CCP4 wiki; if you know the package well, please contribute to it. I eventually dug up what I was looking for in: /opt/ccp4/ccp4-6.0.2/examples/unix/runnable/ or the equivalent on your system. Here, you’ll find a collection of shell scripts, confusingly named with the suffix “.exam”. As an example, here&... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1711726 Mon, 18 Aug 2008 07:30:45 +0100 1711726 http://www.medworm.com/index.php?rid=1709158&cid=t_348399_87_f&fid=34935&url=http%3A%2F%2Fmedicine.com.my%2Fwp%2F%3Fp%3D4105 I spotted this in Wired In a paper that appeared on the PLoS Neglected Tropical Diseases website yesterday, Asif Khan and Olivo Miotto explained that viruses evolve very quickly, which makes it hard for the immune system to recognize them. Working at the National University of Singapore, in collaboration with Johns Hopkins researchers, they sought to identify a few tiny parts of the virus that have remained unchanged for years. Using information from public databases, the team identified forty-two short protein sequences that are shared by almost every single type of dengue fever. Those snippets are just big and distinctive enough to train the immune system so that it can recognize the disease and fight it. One thing that impresses me is how Singapore manages to attract so many expat scie... Malaysian Medical Resources blogs http://www.medworm.com/rss/comments.php?id=1709158 Fri, 15 Aug 2008 04:00:00 +0100 1709158 http://www.medworm.com/index.php?rid=1668856&cid=t_348399_113_f&fid=36670&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmsdn%2Fhealthblog%2F%7E5%2F350992790%2FTechForum2008RedmondBrochure.pdf Would you like to get the latest scoop on HealthVault and Microsoft Amalga?  How about a sneak peek at future health solutions using Microsoft Surface?  Would you like to see how some of the world's leading healthcare organizations are improving workflow collaboration and delighting patients with Microsoft Unified Communications?  Or how about an opportunity to see a clinical user interface built with Microsoft Silverlight?  Would you like to see how Microsoft Dynamics CRM can improve patient loyalty and satisfaction?   Would you like to visit the Microsoft campus in Redmond and meet the executives who are leading our health initiatives around the world?  Would you like to tour the Microsoft Home of the future?  If so, this is your golden ticket.   ... HealthBlog blogs http://www.medworm.com/rss/comments.php?id=1668856 Thu, 31 Jul 2008 00:45:50 +0100 1668856 http://www.medworm.com/index.php?rid=1660825&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F349072450%2F Image via WikipediaIt’s getting pretty clear that GPUs have a big place in the future of molecular simulation (and the cell processor). NAMD, SimTK, Gromacs via Vijay Pande’s Folding@Home, etc are all pursuing acceleration as a core part of their efforts. I have had informal discussions with a few people actively running GPU-based simulations For the first time since MM-PBSA came around and people started applying MD to study large scale molecular motions (just see work by Benoit Roux and Georgios Archontis), I am really encouraged about the state of molecular simulation. GPUs, acceleration and large scale distributed computing, coupled with special purpose machines are poised to give the field a short in the arm. I have always been annoyed by the fragmentation in the field, bu... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1660825 Tue, 29 Jul 2008 04:19:49 +0100 1660825 http://www.medworm.com/index.php?rid=1657216&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F346757907%2F Freebase is a service (I use that word very deliberately) that I have talked about before. I have long had plans for Freebase, but never quite gotten around to doing more than some minor type creation and edits (as opposed to Pierre, who is quite well known with the Freebase crowd). I have also been somewhat annoyed at Freebase’s not quite Semantic Web status and requirement to reside within their environment. Yesterday, at OSCON, I had the chance to listen to a talk by Jamie, Colin and Toby from Metaweb/Freebase. It was a great, enlightening talk, very much a computer science/technology talk, helped by interesting garb (pirate eye patches anyone). I left wanting to go back and play with the system. I really liked the examples that they showed, which really demonstrated the power of ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1657216 Sat, 26 Jul 2008 17:42:34 +0100 1657216 http://www.medworm.com/index.php?rid=1637779&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2F2008%2F07%2F778 The other day, registrars began opening up domain registrations to .me TLDs.  I became aware of this because Beth at PixelRN had a quandary about a domain she was trying to register and the TLD .me obviously caught my eye.  From what I can gather, tons of .me domains are being snagged by the hour at premium prices.  GoDaddy and other registrars are reportedly screwing the pooch either because of higher-than-expected demand or because there has been too much bullshit with front-running where searches basically ‘tip off’ a registrar (and, in my conspiracy-theory-addled brain, an elite group of insider clients who will snag it in the precious waiting period while one decides if they want it or not). I probably won’t get one, but in complete boredom I wondered what kind of... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=1637779 Fri, 18 Jul 2008 16:21:46 +0100 1637779 http://www.medworm.com/index.php?rid=1603100&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F331401054%2F I have nothing to declare except my genius. — Oscar Wilde I must admit that D.E. Shaw makes me go green around the gills. He was a computer science professor at Columbia University, founded a very successful hedge fund (he doesn’t run it full time any more), is the money behind a company that makes some great molecular modeling software, and is the chief scientist at a computational scientific research company. That he also publishes single author theoretical papers is just plain unfair. One of the cooler projects at D.E. Shaw Research is Anton; “a specialized, massively parallel supercomputer designed to execute MD simulations hundreds of times faster than has been possible to date.” Yesterday, the New York Times carried an article on Anton. I have argued in the p... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1603100 Thu, 10 Jul 2008 05:05:09 +0100 1603100 http://www.medworm.com/index.php?rid=1593770&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F07%2F08%2Fthoughts-on-other-programming-languages%2F With respect to their potential for bioinformatics web applications: Feature Python Ruby Modern, clean syntax, object-oriented Yes Yes Web framework Django Rails Bio library BioPython BioRuby Extensive Bio graphics library Not really - any more than this? Kind of - Bio::Graphics Use with App Engine Yes Not yet Well-regarded by scientific programmers Yes ?? To the novice, it looks like “much of a muchness”. Thoughts? (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1593770 Tue, 08 Jul 2008 01:53:38 +0100 1593770 http://www.medworm.com/index.php?rid=1582918&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2F328488940%2Fcompiling_firefox_3_from_sourc.php Responding to the innate human desire to have the faster browser possible, I am almost happy with Firefox 3.  But not quite.  Thus, the experiment: compile from source.  This is accomplished as follows: 0. Kubuntu does not come with the packages necessary to build from source, by default.  You must install a bunch of stuff first.  Fortunately, this is easy.  To install the prerequisites necessary to build Firefox from source, open a terminal and type: apt-get build-dep firefox 1. Download the Firefox source code here. 2.  Extract to a suitable place, likely a subdirectory in your home folder. 3. Open a terminal and go to the subdirectory.   4.  Run the configure script: ./configure --enable-optimize --disable-tests  --enable-gnomevfs --... The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=1582918 Mon, 07 Jul 2008 02:36:25 +0100 1582918 http://www.medworm.com/index.php?rid=1560790&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2F324554170%2Fbrowser_security.php 40% of Internet users do not upgrade their browsers to the most secure version.  Internet Explorer users have the worst record, with more than half having failed to update. OK, people, do your patriotic duty and get with the upgrades!  Then we can see the National Threat Advisory go down to blue, for the first time in history. (source: Ars Technica) Read the comments on this post... (Source: The Corpus Callosum) The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=1560790 Wed, 02 Jul 2008 04:09:04 +0100 1560790 http://www.medworm.com/index.php?rid=1546738&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F320138501%2F Chris Anderson is a man I respect and Wired a magazine I like most of the time. During my chat with Jon Udell, I had bemoaned the gap between science and the general public, and Anderson’s latest article on Wired only serves as a reinforcement of that frustration. In an article entitled The End of Theory: The Data Deluge Makes the Scientific Method Obselete he writes about how the petabyte era is going to change science has one thing very right, and one thing very wrong. He is write more is not more. It is different. But more does not mean the end of the scientific method. I would argue that it allows us to think about new ways to apply the scientific method to try and solve problems. Biology has changed a lot since the 70s, and its not just genetics. The very field has been turned ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1546738 Thu, 26 Jun 2008 01:24:59 +0100 1546738 http://www.medworm.com/index.php?rid=1542979&cid=t_348399_132_f&fid=35016&url=http%3A%2F%2Fpeanutbutter.wordpress.com%2F2008%2F06%2F25%2Fcarmen-a-scalable-science-cloud%2F Paul Watson presents a talk on CARMEN a the Google Seattle Conference on Scalability. (Source: peanutbutter) peanutbutter blogs http://www.medworm.com/rss/comments.php?id=1542979 Wed, 25 Jun 2008 10:05:26 +0100 1542979 http://www.medworm.com/index.php?rid=1543114&cid=t_348399_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2008%2F06%2F24%2Fthe-petabyte-age.aspx The latest issue of Wired magazine includes a series of articles lead by the editor Chris Anderson's article, "The End of Theory: The Data Deluge Makes the Scientific Method Obsolete." In Wired's usually controversial approach to topics, he leads off with the quote, "All models are wrong, but some are useful." In the petabyte age, we move from local storage to storage in the cloud and "information is not a matter of simple three- and four-dimensional taxonomy and order but of dimensionally agnostic statistics."He sites one medical example, he cites Craig Vetner who "went from sequencing individual organisms to sequencing entire ecosystems." He proposes that "We can analyze the data without hypotheses about what it might show."Do these rash statements have relevance to health care? Much of ... eHealth blogs http://www.medworm.com/rss/comments.php?id=1543114 Tue, 24 Jun 2008 09:34:56 +0100 1543114 http://www.medworm.com/index.php?rid=1543222&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2F2008%2F06%2F768 Blog Updates: I’m happy to report all is well. The blog software is updated, making room for all the “current” plug-ins, themes, etc. and most importantly, the security fixes applied so that I don’t get h4×0r5 hijacking the site to something hideous and embarrassing like an online yarn shop. I’d never live that one down. Regarding the slick black theme: yes, it’s understated, and surprisingly, yes, it’s pretty much done. I downloaded it of course, because I can’t create much of anything, but I can always edit and tweak. (which I need to do because I want my links underlined and my blogroll subcategorized) However, I really like the minimal, clean look. Maybe in a month or two I’ll think to add a graphic here and there, but the day ... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=1543222 Tue, 24 Jun 2008 08:18:26 +0100 1543222 http://www.medworm.com/index.php?rid=1535743&cid=t_348399_93_f&fid=34899&url=http%3A%2F%2Fwww.mexicomedstudent.com%2F2008%2F06%2F766 Tonight I plan to upgrade this site to Wordpress 2.5.x. I’ll also be applying a new theme, though I’m not 100% sure which one it will be. I can say, however, that it will NOT be a completed task anytime soon. I’m not a web designer and I don’t want to waste time making things purty. I care more about functionality and such and will be adding a few new plugins as well. So, if there are a few glitches y’all notice over the next 24-48h or so, please PLEASE let me know. Letting me know what you think of the new semi-temporary look and feel as well would make me verrry happy. I may yet continue as a Mexican medical student at another school, so I haven’t given up the domain yet, but it’s time for some serious housecleaning around here. If your blog is n... Mexico Medical Student blogs http://www.medworm.com/rss/comments.php?id=1535743 Sat, 21 Jun 2008 04:01:14 +0100 1535743 http://www.medworm.com/index.php?rid=1526041&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F06%2F19%2Fwell-everyone-else-was-doing-it%2F Everyone seems to be having fun with Wordle. Except for me, until I realised that all my machines were cursed with something named “icedtea-gcjwebplugin”, as opposed to the Sun java plugin. Problem solved. So there it is. But for the prominent “bioinformatics”, you’d never guess I was a biologist, would you. I do believe that this is telling me something. (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1526041 Wed, 18 Jun 2008 14:14:58 +0100 1526041 http://www.medworm.com/index.php?rid=1526042&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F06%2F17%2Flinux-tip-forward-email-from-m-exchange-server-to-gmail%2F My work email has migrated to M$ Exchange Server, with M$ Outlook Web Access. Eurgh. No more POP3 retrieval to my GMail account. I restored sanity using an Ubuntu server as follows. Needless to say, this requires that (a) the exchange server allows IMAP access and (b) the SMTP server for your machine will relay mail outside of your domain. Updated: to do it all via procmailrc, without .forward Install fetchmail and edit /etc/fetchmailrc: sudo apt-get install fetchmail sudo nano -w /etc/fetchmailrc Make /etc/fetchmailrc look something like this: set daemon 300 poll your.exchange.server protocol imap username “user” password “pass” smtpname “user@gmail.com” ssl replacing your.exchange.server, user (exchange), pass (exchange) and user@gmail.com (your ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1526042 Tue, 17 Jun 2008 07:50:25 +0100 1526042 http://www.medworm.com/index.php?rid=1526090&cid=t_348399_109_f&fid=34699&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fscienceblogs%2FvjmG%2F%7E3%2F313568197%2Ffirefox_3_download_day.php I scarcely need to mention it, but today is the big day: Firefox 3 is out, so be sure to download it.  The Mozilla folks are shooting for a world record for the most downloads in a single day. Will Linux Users Miss Out on Firefox 3?  Silly article.  Download the source.  Configure, make, make install. Just order a pizza first, because compiling it from source takes a while.  But so does eating a pizza. Actually, the article does make some good points.  If you want ease of upgrade, and a no-hassle experience, you might wait for your distribution people to make a tested package available. Read the comments on this post... (Source: The Corpus Callosum) The Corpus Callosum blogs http://www.medworm.com/rss/comments.php?id=1526090 Tue, 17 Jun 2008 06:29:45 +0100 1526090 http://www.medworm.com/index.php?rid=1508518&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F308982556%2F One of the cooler moments in my life was when Nick Carr’s publisher sent me an advance copy of The Big Switch, Nick’s book on the future of computing as a utility. Little did I know at the time that a long standing love of all things computing, and my increasing passion for distributed, web scale computing, would collide with my own career path. Not this soon any way. As some of you are aware this is my last week in my current job. Later this month I will be starting a new position in the business development group at Amazon Web Services, where I will jump headfirst into the world of web services and utility computing. Many eons ago, I promised myself, never to take up a job where I didn’t believe in the underlying fundamentals and that has been the case throughout my car... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1508518 Tue, 10 Jun 2008 17:30:57 +0100 1508518 http://www.medworm.com/index.php?rid=1497390&cid=t_348399_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2008%2F06%2F06%2Fautomatic-content-for-the-people%2F Anyone who has ever built a website knows that maintaining it is a lot of work. There’s just making sure it hasn’t gone offline because the httpd daemon died. Constant monitoring for script kiddies and their SQL injections. Not to mention continually feeding it with fresh content, lest your audience become bored and desert. I’ve always thought it would be cool to build a site that could more or less look after itself. There’s a myriad of content management systems to choose from, most of which are somewhat hackable in whatever language they happen to be coded in. One of the more mature in this respect is Drupal - which is the engine behind Eureka! Science News. It’s a fully-automated science news portal, using a bunch of customised Drupal modules to aggregate,... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=1497390 Fri, 06 Jun 2008 11:53:22 +0100 1497390 http://www.medworm.com/index.php?rid=1442957&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F290724664%2F Matt Wood has a great great screencast of a talk around some very relevant problems (things that touch my interests as a blogger and in my day job as well). No surprise that I agree with him on the importance of distributed data and how we can start leveraging the web for a field that gets more and more data intensive by the day. Further reading Do we need life science CDNs? Technorati Tags: Distributed Computing, MapReduce, Distributed Data ShareThis (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1442957 Thu, 15 May 2008 07:00:10 +0100 1442957 http://www.medworm.com/index.php?rid=1442958&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F289829468%2F Nat Torkington has a thoughtful post up on the O’Reilly Radar where he writes about ubiquitous computing (or ubicomp as he calls it). I want to cast that problem a little differently. Let us assume we have a scalable cloud that we can tap into, perhaps with databases that easily scale to support streaming data. Let us imagine a lab, with instruments streaming out data, with devices consuming those data, and systems that can make decisions based on the data they are receiving. Such an interconnected work, a world with pervasive, ubiquitous computing might sound like science fiction, but over the past few years, we have slowly but surely built up the beginnings of an infrastructure that will make this scenario possible, perhaps a lot faster than we thought. The iPhone, the Chumby, the ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1442958 Wed, 14 May 2008 01:10:46 +0100 1442958 http://www.medworm.com/index.php?rid=1434536&cid=t_348399_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F288107211%2F At Accelrys, a lot of the software I managed was in-licensed from academia. That approach allowed the company to tap into the intellectual resources of some of the smartest academic researchers in the world, but it also created a problem. One was the difference in software development practices. Some of the academic code barely had version control. But that’s the obvious one. In a new post at Computing at Scale, Bill McColl writes about Domain-specific parallel programming. Translating code parallelized for an academic setting, often under the assumption that huge clusters might be available, to an industrial setting where scaling and fault tolerance become critical, where resource availability varies widely, and speed is critical, is always a challenge. This is especially true when ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=1434536 Sun, 11 May 2008 15:24:04 +0100 1434536