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'. Sat, 03 Sep 2011 01:50:11 +0100 http://www.medworm.com/index.php?rid=5169512&cid=t_100098_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F008257.html Harvard chemistry professor Alán Aspuru-Guzik has developed software that can find better organic electronic materials. A chemical compound designed with the aid of a Harvard-created computer program has turned out to be one of the best organic electronic materials to date. This new material, an organic semiconductor, could be used to make new electronics such as colorful displays that roll up. It's an important proof of principle for using computers to aid materials design. The article also mentions a computational model used to develop faster charging batteries which A123Systems is in the process of commercializing. Why does this matter? If more advances in batteries, photovoltaic materials, and other important areas for materials could be done with computational experiments rather with... FuturePundit blogs http://www.medworm.com/rss/comments.php?id=5169512 Fri, 26 Aug 2011 23:00:00 +0100 5169512 http://www.medworm.com/index.php?rid=5159275&cid=t_100098_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FRTT7SAYwins%2F As long as there have been EMRs, there have been vendors selling aggregated, de-identified data. And there have been people worried about privacy. That issue came up last week AHIMA Legal EHR Summit right here in Chicago, during a session exploring issues related to data ownership and stewardship in the era of cloud computing. (I’ll have a more complete rundown of the session Monday in InformationWeek Healthcare.) Near the start of the panel, Daniel Orenstein, senior VP and general counsel of Athenahealth tried to put any lingering questions to rest right away. “I think data monetization is kind of a red herring,” Nussbaum said of people who criticize vendors for selling sensitive patient information. According to Nussbaum, de-identified data no longer includes any protec... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=5159275 Sun, 21 Aug 2011 12:52:18 +0100 5159275 http://www.medworm.com/index.php?rid=5107465&cid=t_100098_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F008228.html The US Defense Advanced Research Projects Agency is spending money to come up with counters to the threat that chips in servers, PCs, routers, and other computer equipment could contain Trojans. The Pentagon’s top research division is trying, however. Over the past two months, Darpa, has awarded nine contracts totaling $49 million for its Integrity and Reliability of Integrated Circuits (IRIS) program to check for compromised chips. Seven companies and two universities received the awards. Companies create clones of chips made by other companies. Some unethical companies even make counterfeit memory cards which have prompted the development of software to test USB memory sticks for fakes which perform worse than the real thing and which fail at higher rates. There's even... (Source: ... FuturePundit blogs http://www.medworm.com/rss/comments.php?id=5107465 Sat, 06 Aug 2011 23:00:00 +0100 5107465 http://www.medworm.com/index.php?rid=5062525&cid=t_100098_180_f&fid=38607&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fsuccessbeginstoday%2FBHWQ%2F%7E3%2FCEhqG7Kd9sI%2F This was our second theme based week on Success Begins Today. The theme was communication and featured a free book giveaway. Theme: Communication Monday: Making A True Connection We all communicate, but do we truly connect? Tuesday: Communicating Your Title The words you use in your title say a lot about you. Choose wisely. Thursday: Google Plus: What Will You Write? A post about creating your about page for Google Plus and the Throne of Agony. Friday: Good Morning, Mike Guest post by Sarah McGaugh on using a greeting to change someone’s life. Links mentioned during the week: Everyone Communicates, Few Connect. Sally Hogshead Fascinate Test Throne of Creative Agony Career Builder Article Google Plus Bird in your Hand Additional References: John Maxwell: Everyone Communicates Book Page K... Success Begins Today blogs http://www.medworm.com/rss/comments.php?id=5062525 Sun, 24 Jul 2011 15:16:23 +0100 5062525 http://www.medworm.com/index.php?rid=4934666&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FYfHJ5LxKF7I%2F Tweet Earlier today I visited DBMS Musings to read Daniel Abadi’s blog post on peer review, but ended up re-reading an older post. In the post Daniel talks about why he is doing a startup pre-tenure. I am not an academic, neither have I ever started a company, although I’ve been in both environments, so I can’t quite speak from experience here, but the post caught my attention at multiple levels. What makes this interesting is that Daniel has spent time on getting his company off the ground himself, with active involvement, and the resulting leave of absence limits his ability to do things junior faculty are expected to do, like publish. He admits that there is little precedent and that it’s a gamble. So why go on? Admittedly, this is computer science, but the key ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4934666 Sun, 12 Jun 2011 06:44:50 +0100 4934666 http://www.medworm.com/index.php?rid=4911621&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fnew-apple-developments-will-likely-spur-mobile-health-innovation If you’re reading this blog, you most likely saw the pop-up/interstitial Intel ad that asks “Is Cloud Computing Right for You?” Steve Jobs apparently thinks so. The Apple impresario announced the company’s most talked-about offering, iCloud, at its Worldwide Developers Conference this week, among a number of other new developments that have stirred Apple fans to new heights of evangelism. Mashable.com staffers have been keeping up with conference developments and announcements pretty well. No sticky read more (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4911621 Tue, 07 Jun 2011 14:11:59 +0100 4911621 http://www.medworm.com/index.php?rid=4902616&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FUPd_4dJzp1g%2F Tweet I would suggest that all my friends in the world of bioinformatics read this fabulous article by Pat Helland. Pat’s on of the leading experts in distributed transactions and knows more about databases than most of us put together. His ACM article goes into some the tradeoffs and changes in mindset that need to me made when working with data that changes and comes from different sources, and all so o ften has ambiguity associated with it. It also tells you a little but about the differences in SQL and NoSQL systems when it comes to transaction semantics and in a way that meets complete sense. Perhaps the most interesting part of the article was the section on “Mulligan stew” where we also provides the example of building a heterogeneous catalog. A product catalog... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4902616 Mon, 06 Jun 2011 19:16:36 +0100 4902616 http://www.medworm.com/index.php?rid=4883533&cid=t_100098_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F008112.html While serving time at the Jixi labor camp in China Liu Dali and other prisoners were forced to play video games to earn virtual credits in games like World of Warcraft . Guards then sold those virtual credits for profit. Liu says he was one of scores of prisoners forced to play online games to build up credits that prison guards would then trade for real money. The 54-year-old, a former prison guard who was jailed for three years in 2004 for "illegally petitioning" the central government about corruption in his hometown, reckons the operation was even more lucrative than the physical labour that prisoners were also forced to do. It is bad enough that some teenagers get addicted to... (Source: FuturePundit) FuturePundit blogs http://www.medworm.com/rss/comments.php?id=4883533 Mon, 30 May 2011 23:00:00 +0100 4883533 http://www.medworm.com/index.php?rid=4883814&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FDCMLe-cIKq4%2F Tweet Computing is critical. Computing is not important. Two seeming contradictory statements, but I’ll point to Google. Their success is built on computing, lots of it. The end user doesn’t care. They get information back. They don’t have to set up clusters and queries. They just search. While that’s a gross oversimplication for science, there are aspects of computing productivity that just don’t make sense anymore. I was reminded of this point by a question on Biostar about setting up MPI. There are different level of skill sets required and I might be one of the first to argue that a computational scientist should understand their tool, the computer. But at what level? In the end I love abstractions and productivity. The more you have to spend time setti... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4883814 Sun, 29 May 2011 17:05:22 +0100 4883814 http://www.medworm.com/index.php?rid=4872201&cid=t_100098_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FwDgU7yJHDwM%2F That’s the question I ask in my weekly post for EMR and HIPAA. Check it out, and share your opinion. Related posts:Another black eye for EHRs EHRs in the public eye EHRs and other health IT on the national radar screen (Source: Neil Versel's Healthcare IT Blog) Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=4872201 Thu, 26 May 2011 20:28:17 +0100 4872201 http://www.medworm.com/index.php?rid=4872204&cid=t_100098_113_f&fid=34634&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FEmrAndHipaa%2F%7E3%2FM2lKprj3Yl8%2F A blog post today by Microsoft’s Dr. Bill Crounse got me thinking again about the cloud. Crounse cited a new CDW poll showing that 30 percent of healthcare organizations could be considered “cloud adopters,” and for good reason. “The flexibility, scalability and lower costs associated with moving certain line of business applications to the cloud are compelling, especially for an industry like healthcare. After all, the primary focus of hospitals and clinics is caring for patients, not running an IT empire. There’s not a CIO, CFO, CEO, COO, CNO, CMIO, or CMO who wouldn’t love to shift some of their IT spending to delivering better care to the communities they serve,” Crounse wrote. They were more likely to turn to the cloud for “commodity” serv... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4872204 Thu, 26 May 2011 20:25:03 +0100 4872204 http://www.medworm.com/index.php?rid=4852855&cid=t_100098_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fwhy-cloud-computing-can-be-dangerous-in-healthcare%2F2011.05.23 A lot of people are intrigued with using “cloud” applications and storage for personal health data. This week we’re seeing what I think is the final nail in the coffin of “cloud only” for anything important. You gotta have offline backups: two huge cloud vendors – Amazon and now Google – have demonstrated that even they can go down, leaving their users absolutely powerless. Cloud computing (Wikipedia) is hugely attractive to software developers and businesses. As shown in this diagram from Wikipedia, the idea is that you do your computing using storage or tools that are on some computer somewhere out there “in the cloud.” You don’t know or care where, because somebody out there takes care of things. As your business or database grows, “they” take care of it. And it... Better Health blogs http://www.medworm.com/rss/comments.php?id=4852855 Mon, 23 May 2011 18:00:31 +0100 4852855 http://www.medworm.com/index.php?rid=4841830&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F05%2F18%2Fhow-to-create-a-partial-ucsc-genome-mysql-database%2F File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4841830 Wed, 18 May 2011 04:54:10 +0100 4841830 http://www.medworm.com/index.php?rid=4841673&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fshould-we-abandon-cloud It's been a bad month for the cloud. First there was the major Amazon EC2 (Elastic Cloud) outage April 21-22 that brought down many business and websites. Some of the data was unrecoverable and transactions were lost. No sticky read more (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4841673 Mon, 16 May 2011 13:40:07 +0100 4841673 http://www.medworm.com/index.php?rid=4813409&cid=t_100098_113_f&fid=34695&url=http%3A%2F%2Fmedicalconnectivity.com%2F2011%2F05%2F10%2Fstorms-from-the-cloud%2F Given the analogy between actual clouds and computer clouds, it now seems appropriate to extend the concept to storms that those clouds may bring. This was illustrated recently (April 21, 2011) when Amazon had a cloud outage (a mixed metaphor no doubt) in their Amazon Web Services business. This situation was covered by the NY Times (here), and the professional computer press (here) among others. As a result of Amazon’s problems some Web sites were reported to be down for as long as 11 hours, although actual loss of previously stored information has seemingly not been part of the problem–this time. However there is a related question for any new data that was or should have been generated during the outage. Where is it, and will the gap be properly filled in retroactively? The ... Medical Connectivity Consulting blogs http://www.medworm.com/rss/comments.php?id=4813409 Tue, 10 May 2011 23:07:19 +0100 4813409 http://www.medworm.com/index.php?rid=4794932&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcloud-computing-or-data-center-how-hospitals-should-analyze-their-health-it-storage-needs No sticky read more (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4794932 Fri, 06 May 2011 17:28:19 +0100 4794932 http://www.medworm.com/index.php?rid=4789399&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fdata-security-debate-here-stay One of the biggest ongoing debates in the HIT world is how best to protect digitized health information. And based on the findings of a new survey, it seems safe to say that even as technology advances, those debates are going to continue. The survey comes from the Ponemon Institute, and in looking at the issue of data security as more people take to cloud computing, it finds just a small disagreement between cloud computing vendors and their prospective clients. No sticky read more (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4789399 Wed, 04 May 2011 13:26:03 +0100 4789399 http://www.medworm.com/index.php?rid=4771358&cid=t_100098_180_f&fid=38607&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fsuccessbeginstoday%2FBHWQ%2F%7E3%2FoQXVs9bvmvs%2F I noticed something very curious Friday in the financial news. Microsoft’s stock dropped over 5% in one day. The headline went on to say that the main culprit was the drop in sales of the windows operating system. The largest drop was in netbook sales which were down a whopping 40%. The main reason given was the adoption of tablet computers… Specifically Apple iPads. Apple actually had larger net income figures than Microsoft. It seems like people are opting for the more convenient touch screens of a tablet computer than a laptop or netbook computer. This has certainly been the case for me. I get most all of my news and information on the iPad as well as Email, Facebook and Twitter. My old netbook hasn’t seen the light of day for months. My laptop gets occasional use, bu... Success Begins Today blogs http://www.medworm.com/rss/comments.php?id=4771358 Sat, 30 Apr 2011 19:29:43 +0100 4771358 http://www.medworm.com/index.php?rid=4768038&cid=t_100098_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fcurrent-science-news-2.html Uranium hard drive – A new uranium-containing compound maintains its magnetic behaviour at low temperatures. The discovery could take us a step closer to magnetic memory devices with capacities thousands of times denser than current high-end hard drives. Clouds from both sides – Atmospheric and climate models may have overlooked the fact that exactly how clouds appear to reduce the amount of sunlight available for warming the surface of the earth depends on the wavelength being measured across the spectrum from infrared to ultraviolet. The finding could now help researchers improve climate models by factoring in the effects of cloud cover more precisely. Soap story – It is perhaps no real surprise to any chemist who has unblocked a drain clogged with white lardy deposits,... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4768038 Fri, 29 Apr 2011 08:19:59 +0100 4768038 http://www.medworm.com/index.php?rid=4734452&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F19%2Fwhy-cant-pubmed-or-academic-journals-get-the-basics-right%2F A recent question at BioStar asked “Is the NAR database list available in a computer readable format?” The short answer is “no” and Pierre has done some excellent preliminary work to address the issue. I’ve been working on a database and web application to check the associated URLs but quite frankly, this is tedious, a waste of everyone’s time and could be entirely avoided if the publishing industry did a better job. All that’s required is that either NAR or PubMed provide structured data – XML, Medline format, I don’t care what – containing a field that looks something like this: URL http://a.valid.url.goes.here That way, we could all avoid writing regular expressions to detect URLs in abstracts. No wait – to detect brok... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4734452 Tue, 19 Apr 2011 04:45:29 +0100 4734452 http://www.medworm.com/index.php?rid=4714947&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F15%2Fr-2-12-to-2-13-package-upgrade%2F If you: use Linux have just upgraded your R installation from 2.12 to 2.13 installed some/all of your packages in your home area (e.g. ~/R/i486-pc-linux-gnu-library/2.12) and… …are wondering why R can’t see them any more just do this: # at a shell prompt cp ~/R/i486-pc-linux-gnu-library/2.12 ~/R/i486-pc-linux-gnu-library/2.13 # in R console update.packages(checkBuilt=TRUE, ask=FALSE) # back to the shell rm -rf ~/R/i486-pc-linux-gnu-library/2.12 Filed under: computing, linux, R, statistics Tagged: how to, ubuntu, upgrade (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4714947 Fri, 15 Apr 2011 04:00:47 +0100 4714947 http://www.medworm.com/index.php?rid=4693447&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F04%2F08%2Ffixing-aberrant-files-using-r-and-the-shell%2F Once in a while, you embark on what looks like a simple computational procedure only to encounter frustration very early on. “I can’t even read my file into R!” you cry. Step back, take a deep breath and take note of what the software is trying to tell you. Most times, you’ve just missed something very straightforward. Here’s an example. Recently, I was trying to retrieve some data describing characteristics of microbial genomes from the NCBI FTP site. The file, lproks_0.txt (direct link), looked like a regular tab-delimited file with a couple of header lines: head lproks_0.txt ## Microbial Organism Information Page ## Columns: "RefSeq project ID" "Project ID" "Taxonomy ID" "Organism Name" "Super Kingdom" &qu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4693447 Fri, 08 Apr 2011 04:41:37 +0100 4693447 http://www.medworm.com/index.php?rid=4684638&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FrSNtgf1kFnE%2F Tweet I have long channeled Jeff Jonas and his ideas around on data finds data. His recent blog post on the data being the query extends some of those thoughts. I find this trend fascinating, although I favor the just in time data approach, since not all information needs to be acted upon instantly, but the broader point holds. I had a similar discussion with Richard Durbin recently around data first science, where we discussed collecting data and then querying it to generate hypotheses and to see how the new data impacted existing knowledge. It’s going to be interesting how today’s life science data systems evolve. The data-driven approach which I talk about a lot is one that is essential for modern biological research (saw a great talk on this by Joel Dudley recently); usi... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4684638 Tue, 05 Apr 2011 13:54:59 +0100 4684638 http://www.medworm.com/index.php?rid=4658438&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Frx-md-emr-1-tab-qd Billions in stimulus dollars have many physicians now eyeing electronic medical record software for their practices. Hospitals are installing EMRs (for providers?) too. Unfortunately for many who practice care, EMRs are still a pretty bitter pill to swallow. read more (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4658438 Wed, 30 Mar 2011 19:58:21 +0100 4658438 http://www.medworm.com/index.php?rid=4653491&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FX92wTUvET3w%2F Tweet The scale of modern life science research, where scale is not just about data volume, but also about rate of change, number of users, geographic scale, etc means that resources have to look at how they provide services differently and, more importantly, funding agencies and philanthropists have to decide where to draw the line. Is this an opportunity for commercial efforts? Is the market ready to do this, or are they willing to live with overall inefficiencies and limitations? Is there a tiered model that would be acceptable. Recent discussions and observations of what various companies and orgs are doing leads me to believe that we need to really think hard about overall efficiencies and consider the value of time. More later (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4653491 Tue, 29 Mar 2011 07:03:03 +0100 4653491 http://www.medworm.com/index.php?rid=4552124&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F3JkrNEoA2Ks%2F Tweet A couple of great posts on the Metamarkets blog recently that might be of relevance to the bioinformatics crowd. The first one, by Mike Driscoll, talks about lessons for building a petabyte data platform. Their four guiding principles Experiment often, fail fast Keep things simple to scale well Keep things modular to accommodate change Avoid undifferentiated heavy lifting I still feel that the data systems we have in the life science domain aren’t doing enough to learn good lessons from the web world, which is embracing change, complexity and scale, and even small teams, like the one at Metamarkets is able to do a lot with less, due to the kinds of principles mentioned in the post. One of the problems I see in informatics is a lack of appreciation for some of the skill... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4552124 Sat, 05 Mar 2011 19:38:59 +0100 4552124 http://www.medworm.com/index.php?rid=4545119&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F03%2F04%2Fruby-version-manager-the-absolute-basics%2F Confession: I’m still using Ruby version 1.8.7, from the Ubuntu 10.10 repository. Why? I have a lot of working code, I don’t know how well it works using Ruby 1.9 and I’m worried that migration will break things and make me miserable. Various people have pointed me to RVM – Ruby Version Manager. As the name suggests, it allows you to manage multiple Ruby versions on your machine. Today, I needed to test an application written for Ruby 1.9.2, so I used RVM for the first time. Here are the absolute basics, for anyone who just wants to test some code using Ruby 1.9, without messing up their existing system: # install rvm bash < <( curl http://rvm.beginrescueend.com/releases/rvm-install-head ) # add it to your .bashrc echo '[[ -s "$HOME/.rvm/scripts/rvm&quot... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4545119 Fri, 04 Mar 2011 05:12:36 +0100 4545119 http://www.medworm.com/index.php?rid=4545033&cid=t_100098_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2011%2F03%2F03%2Fonline-predictive-tools-for-mental-illness-the-optimi-projec.html OPTIMI is a r&d project funded by the European Commission under funded by the European Union's 7th Framework Programme "Personal Health Systems - Mental Health" .The project has two key goals goals: a) the development of new tools to monitor coping behavior in individuals exposed to high levels of stress; b) the development of online interventions to improve this behavior and reduce the incidence of depression.To achieve its first goal, OPTIMI will develop technology-based tools to monitor the physiological state and the cognitive, motor and verbal behavior of high risk individuals over an extended period of time and to detect changes associated with stress, poor coping and depression.  A series of “calibration trials” will allow the project will test a broad range of tec... Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=4545033 Thu, 03 Mar 2011 18:03:00 +0100 4545033 http://www.medworm.com/index.php?rid=4540535&cid=t_100098_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2011%2F03%2Fvladimir-putin-may-be-known-for-showing.html Vladimir Putin may be known for showing off his pectorals riding horses bare chested, but he also seems to have a substantial amount of gray matter between the ears.Our country, including the healthcare IT sector, could probably learn something from him:A Walled Wide Web for Nervous Autocrats Wall Street JournalJan. 8, 2011By EVGENY MOROZOVAt the end of 2010, the "open-source" software movement, whose activists tend to be fringe academics and ponytailed computer geeks, found an unusual ally: the Russian government. Vladimir Putin signed a 20-page executive order requiring all public institutions in Russia to replace proprietary software, developed by companies like Microsoft and Adobe, with free open-source alternatives by 2015.The move will save billions of dollars in licensing fees, but ... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4540535 Thu, 03 Mar 2011 02:15:00 +0100 4540535 http://www.medworm.com/index.php?rid=4532487&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F03%2F01%2Fthe-rstudio-ide-first-impressions-are-positive%2F Integrated development environments (IDEs) are software development tools, providing an interface that enables you to write, debug, run and view the output of your code. Whether you need an IDE or find them useful depends very much on your own preferences and style of working. In my own case for example, I’ve tried both Eclipse and NetBeans, but I find them bloated and rather “overkill”. On the other hand, my LaTeX productivity shot up when I started to use Kile. Most of my coding involves either Ruby or R, written using Emacs. For Ruby (including Rails), I use a bundled set of plugins named my_emacs_for_rails, which includes the Emacs Code Browser (ECB). For R, I occasionally use Emacs Speaks Statistics (ESS), but I’m just as likely to run code from a terminal or u... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4532487 Tue, 01 Mar 2011 02:56:22 +0100 4532487 http://www.medworm.com/index.php?rid=4477672&cid=t_100098_87_f&fid=34902&url=http%3A%2F%2Fwww.futurepundit.com%2Farchives%2F007907.html An article by John Markoff in the New York Times looks at the implications for an expected defeat of the best human Jeopardy players by an IBM Watson computer. IBM's chess-playing software has already beat the best human chess players. But Jeopardy is harder for a computer to play because the computer has to decipher the meaning of the English language question and find the answer in a large pool of information. The implications of progress in A.I. are being brought into sharp relief now by the broadcasting of a recorded competition pitting the I.B.M. computing system named Watson against the two best human Jeopardy players, Ken Jennings and Brad Rutter. Watson is an effort by I.B.M. researchers to advance... (Source: FuturePundit) FuturePundit blogs http://www.medworm.com/rss/comments.php?id=4477672 Tue, 15 Feb 2011 00:00:00 +0100 4477672 http://www.medworm.com/index.php?rid=4473053&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F14%2Fgetting-stuff-into-mongodb%2F One of the aspects I like most about MongoDB is the “store first, ask questions later” approach. No need to worry about table design, column types or constant migrations as design changes. Provided that your data are in some kind of hash-like structure, you just drop them in. Ruby is particularly useful for this task, since it has many gems which can parse common formats into a hash. Here are 3 quick examples with relevance to bioinformatics. 1. JSON JSON is a good fit for MongoDB; when you view a document (represented internally as BSON), the structure looks just the same as the original JSON. I use json/pure as in this example, which grabs expression data for a gene from the Gene Expression Atlas API: require 'open-uri' require 'json/pure' require 'mongo' db = Mongo::Conn... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4473053 Mon, 14 Feb 2011 06:52:41 +0100 4473053 http://www.medworm.com/index.php?rid=4473054&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F13%2Fdumped-on-by-data-scientists%2F A story in The Chronicle of Higher Education reminded me that I’ve been meaning to write about “data science” for some time. The headline to the story: “Dumped On by Data: Scientists Say a Deluge Is Drowning Research” Rather amusingly, this is abbreviated in the URL to “Dumped-On-by-Data-Scientists”; a nice example of how the same words, broken in the wrong place, can lead to a completely different meaning. Anyway, to the point. The term “data scientist” – a good thing, or not? I’m throwing this one out there because I spent much of 2010 (a) reading articles that used the term and (b) trying to decide whether I like it or not – and I still can’t decide. Arguments for: It’s an attention-grabber, designed t... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4473054 Sun, 13 Feb 2011 05:43:21 +0100 4473054 http://www.medworm.com/index.php?rid=4455410&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F09%2Falgorithms-running-day-and-night%2F Warning: contains murky, somewhat unstructured thoughts on large-scale biological data analysis Picture this. It’s based on a true story: names and details altered. Alice, a biomedical researcher, performs an experiment to determine how gene expression in cells from a particular tissue is altered when the cells are exposed to an organic compound, substance Y. She collates a list of the most differentially-expressed genes and notes, in passing, that the expression of Gene X is much lower in the presence of substance Y. Bob, a bioinformatician in the same organisation but in a different city to Alice, is analysing a public dataset. This experiment looks at gene expression in the same tissue but under different conditions: normal compared with a disease state, Z Syndrome. He also notes ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455410 Wed, 09 Feb 2011 03:41:21 +0100 4455410 http://www.medworm.com/index.php?rid=4442078&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FfIV7JtZnFas%2F Tweet This talk from Jeff Hammerbacher is worth a listen. Gives you a good history of enterprise data challenges and some of the reasons why Hadoop became a big deal so quickly and a good sense of the evolving Hadoop ecosystem Jeff Hammerbacher on Evolving a New Analytical Platform – Orbitz IDEAS from Orbitz IDEAS on Vimeo (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4442078 Sun, 06 Feb 2011 05:35:47 +0100 4442078 http://www.medworm.com/index.php?rid=4406053&cid=t_100098_180_f&fid=38607&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fsuccessbeginstoday%2FBHWQ%2F%7E3%2F6GM8rgOzRnk%2F In my last post, I talked about how to get a job promotion. It all comes down to “Making your boss look good.” The post listed books that will help you make your boss look good on paper, in numbers, and on the screen. While making your boss look good is important, you need to keep a few things in reserve. You need your own secret weapon. While you need to make your boss look good, you need to be able to look incredible. So how do you do this? Here is a little known secret that can take YOUR documents, spreadsheets, and presentations to a whole new level. Just pick up this book, download the templates, and go for it. The author, Stephanie Krieger, helps you take your documents to the next level by using the interactive tools in Microsoft Office. She’ll show you how to take your outli... Success Begins Today blogs http://www.medworm.com/rss/comments.php?id=4406053 Thu, 27 Jan 2011 15:02:46 +0100 4406053 http://www.medworm.com/index.php?rid=4405960&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-22-friendfeed%2F In part 1, I described some frustrations arising out of a work project, using the Array Express API. I find that one way to deal mentally with these situations is to spend some time on a fun project, using similar programming techniques. A potential downside of this approach is that if your fun project goes bad, you’re really frustrated. That’s when it’s time to abandon the digital world, go outside and enjoy nature. Here then, is why I decided to build another small project around FriendFeed, how its failure has led me to question the value of FriendFeed for the first time and why my time as a FriendFeed user might be up. At the beginning of each year, I frequently experience a period of angst with respect to my social network and other web activity. Specifically, I ask... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405960 Thu, 27 Jan 2011 09:06:30 +0100 4405960 http://www.medworm.com/index.php?rid=4405961&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fapis-have-let-me-down-part-12-arrayexpress%2F The API – Application Programming Interface – is, in principle, a wonderful thing. You make a request to a server using a URL and back come lovely, structured data, ready to parse and analyse. We’ve begun to demand that all online data sources offer an API and lament the fact that so few online biological databases do so. Better though, to have no API at all than one which is poorly implemented and leads to frustration? I’m beginning to think so, after recent experiences on both a work project and one of my “fun side projects”. Let’s start with the work project, an attempt to mine a subset of the ArrayExpress microarray database. 1. Introduction ArrayExpress is an online database of microarray experiments, organised by both gene (the expression at... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405961 Thu, 27 Jan 2011 09:04:11 +0100 4405961 http://www.medworm.com/index.php?rid=4405962&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F01%2F27%2Fdoes-your-linkedin-map-say-anything-useful%2F LinkedIn, the “professional” career-oriented social network, is one of those places on the Web where I maintain a profile for visibility. I’m yet to gain any practical value whatsoever from it. That said, I know plenty of people who do find it useful – mostly, it seems, those living near the north-east or west coast of the USA. My LinkedIn Network LinkedIn have something of a reputation for innovation – see LinkedIn Labs, their small demonstration products, for example. The latest of these is named InMaps. It’s been popping up on blogs and Twitter for several days. Essentially, it creates a graph of your LinkedIn network, applies some community detection algorithm to cluster the members and displays the results as a pretty, interactive graphic that you c... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4405962 Thu, 27 Jan 2011 04:40:24 +0100 4405962 http://www.medworm.com/index.php?rid=4394771&cid=t_100098_180_f&fid=38607&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fsuccessbeginstoday%2FBHWQ%2F%7E3%2FbN0uHoNPmx8%2F Do you have a desire to move up the ladder at work, to stand out among your peers? Do you know the number one way to do this? It’s actually rather simple. Just make your boss look good. If you do, your boss will notice YOU. There are many ways to do this, but one of the easiest and most productive ways to accomplish this task is to make them look good on paper. If you produce documents for your boss, they need to be stellar and stand out from the crowd. If your boss produces his or her own documents you need to show your boss how to make them exceptional. To do this is rather simple… all you need is a … Secret Weapon Luckily the secret I’m about to tell you doesn’t cost much, or take much time to learn. It’s a step-by-step process that can make you stand out from the crowd in ... Success Begins Today blogs http://www.medworm.com/rss/comments.php?id=4394771 Mon, 24 Jan 2011 14:55:42 +0100 4394771 http://www.medworm.com/index.php?rid=4318392&cid=t_100098_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2011%2F01%2F06%2Fa-year-in-review-perspective-from-higher-education%2F Lev Gonick, CIO of Case Western Reserve University, has written 2011: The Year Ahead in IT, a fresh perspective looking forward instead of back. There are many parallels to healthcare. 1. The Big Picture: The State of the Global Economy and What It Means for IT on U.S. College Campuses (or, globalization and localization). He says that universities are tied to the cities they live in and community partnerships are crucial for global competitiveness. The same could be said for urban and academic medical centers. 2. How do you spell opportunity? A-U-S-T-E-R-I-T-Y (shared services and entrepreneurship).  With greater austerity in health care, shared services and making IT a profit center through entrepreneurship are key to IT survival in healthcare as well. 3. Operational Excellence Is Goo... eHealth blogs http://www.medworm.com/rss/comments.php?id=4318392 Fri, 07 Jan 2011 03:18:50 +0100 4318392 http://www.medworm.com/index.php?rid=4314084&cid=t_100098_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2011%2F01%2F05%2Finterstress-video-released.html We have just released a new video introducing the INTERSTRESS project, an EU-funded initiative that aims to design, develop and test an advanced ICT-based solution for the assessment and treatment of psychological stress. The specific objectives of the project are:Quantitative and objective assessment of symptoms using biosensors and behavioral analysisDecision support for treatment planning through data fusion and detection algorithmsProvision of warnings and motivating feedback to improve compliance and long-term outcomesCredits: Virtual Reality Medical Institute (Source: Positive Technology Journal) Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=4314084 Wed, 05 Jan 2011 12:12:00 +0100 4314084 http://www.medworm.com/index.php?rid=4294753&cid=t_100098_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2F-Xob9ZUrOJc%2Fdell-to-buy-imaging-firm-insite-one.html I've just learned that Dell is making a deeper push into health IT by announcing an acquisition of cloud-based PACS and medical imaging systems vendor InSite One. (Source: Neil Versel's Healthcare IT Blog) Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=4294753 Wed, 22 Dec 2010 23:02:06 +0100 4294753 http://www.medworm.com/index.php?rid=4265954&cid=t_100098_113_f&fid=39280&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMarkHawker%2F%7E3%2FdHxvhvhME3I%2F2351726705 Having watched a presentation by Prabhakar Raghavan, Chief Scientist at Yahoo!, I am becoming increasingly-excited about my decision to study for an MA in Social Research. Coming from a Computer Science background I have recognised that my future will be inhibited by not being able to articulate my work in terms of the social. Prabhakar sees the bigger question as being “not about what can be computed, but what consumers will do with computing”. I fully agree. One issue that we currently face in joining the two disciplines is that their language is just so different, even with definitions of “complexity” and “measurement”. Computer Science does not fully appreciate, with the notable exception of Human-Computer Interaction, the social or behavioural but has built incredible met... Mark My Words 2.1 blogs http://www.medworm.com/rss/comments.php?id=4265954 Fri, 17 Dec 2010 22:10:00 +0100 4265954 http://www.medworm.com/index.php?rid=4253377&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F12%2F13%2Fa-timely-reminder-to-use-strong-passwords%2F You may have read about a security breach at Gawker Media, the company behind several websites including Lifehacker. The server files have been posted at various locations around the web, so I thought I’d take a look. Finding your own email address and decrypted password in a file obtained online is a sobering experience, I can tell you. Fortunately, it was not a password that I use elsewhere, so no damage done. It was, however, a ridiculously “soft” password (all digits, if you must know). Of course, my thoughts soon turned to data analysis. A quick and dirty bash one-liner reveals the top 10 passwords: cut -d " " -f 3 parsed_db.txt | \ awk '{count[$1]++}END{for(j in count) print j,""count[j]""}' | \ sort -nrk2 | head 123456 3057 password ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4253377 Mon, 13 Dec 2010 13:54:49 +0100 4253377 http://www.medworm.com/index.php?rid=4253378&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F12%2F13%2Fcan-a-journal-make-a-difference-lets-find-out%2F Academic journals. Frankly, I’m not a big fan of any of them. There are too many. They cost too much. Much of what they publish is inconsequential, read by practically no-one or just downright incorrect. Much of the rest is badly-written and boring. The people who publish them have an over-inflated sense of their own importance. They’re hidden behind paywalls. And governed by ludicrous metrics. The system by which articles are accepted or rejected is arcane and ridiculous. I mean, I could go on… No, what really troubles me about journals is that they only tell a very small part of the story – the flashy, attention-grabbing part called “results”. We learn from high school onwards that a methods section should be sufficient for anyone to reproduce the resu... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4253378 Mon, 13 Dec 2010 11:34:13 +0100 4253378 http://www.medworm.com/index.php?rid=4207448&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJeaBTmDAQKQ%2F Tweet One of the most frustrating aspects about computational biology and chemistry for me used to be the lack of a hacker culture. Never is that more apparent to me than when I am listening to podcasts like The Changelog or Ruby 5. However, I am upbeat about that changing, despite the odds. There is a good subculture of people in the life sciences who care about good software, building good “products”, even if they are used only internally. Among the circles I hang around in, there is interest in bursty work, APIs, open source libraries, sharing best practices and building a community of programmers and developers, regardless of subfield. I look forward to the day that we have a thriving community of data scientists, software engineers, and systems engineers all coming toget... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4207448 Sun, 28 Nov 2010 03:14:59 +0100 4207448 http://www.medworm.com/index.php?rid=4190391&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FpyRwwH5ybvg%2F Tweet I have now stopped maintaining the current deepaksingh.net. All content is now shared between my main github site and wiki (I do need to update domains, etc, but that will take some more time). Specifically, I continue to maintain two resources of interest to bbgm readers Computing in the Cloud: This is a running list of scientific/parallel/distributed computing frameworks and platforms for Amazon EC2. Life Science Apps on AWS: List of apps I am aware of that run on AWS. Since this is git, I encourage and welcome forking and pull requests. Hopefully these two pages can become resources for the scientific computing and life science computing communities. Important note: These are not official AWS resources, just a list of resources that I try and keep updating for my own perso... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4190391 Sun, 21 Nov 2010 20:23:21 +0100 4190391 http://www.medworm.com/index.php?rid=4168128&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F16%2Fdropbox-tip-continued-convert-a-file-tree-to-html%2F A couple of posts ago, I outlined a small bash script to generate an index.html file, containing links to other files in a directory. This was for generating links to files in a Dropbox public directory. I had completely forgotten about the very useful UNIX/Linux command named tree. If not installed, it should be in your distribution repository (e.g. sudo apt-get install tree for Ubuntu/Debian). Then simply: cd Dropbox/Public/mydirectory tree -H . > index.html Next, navigate to index.html at the Dropbox website and you should see something like the tree on the right. It’s a little ugly and obviously, not as convenient as something like Github, but can be a good quick and dirty fix if you need to share a hierarchy of directories and files. Filed under: computing, linux, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4168128 Tue, 16 Nov 2010 02:29:37 +0100 4168128 http://www.medworm.com/index.php?rid=4152098&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F09%2Fhow-open-source-and-biostar-saved-a-project%2F This is the story of how an open source project and a science communication tool combined to save the day. 1. November 2nd 2010 I receive an email from colleagues at my previous workplace. They are trying to publish some proteomics data and the journal has stipulated that raw data and “annotated peptide mass fingerprint spectra” must be made available. The data that they have come from a machine called a Voyager-DE STR MALDI-TOF mass spectrometer. They are binary files with the suffix “.dat”. No-one is quite sure what to do with them. To plot the spectra we need a file that contains, as a minimum, the intensity and m/z ratio for each peak. Oh, that we had simple CSV files, or at least something in plain ASCII text. 2. November 5th 2010 I get to work. Some web searc... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4152098 Tue, 09 Nov 2010 13:15:22 +0100 4152098 http://www.medworm.com/index.php?rid=4152099&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F11%2F09%2Fa-quick-bash-tip-add-an-index-html-file-to-a-dropbox-public-folder%2F You know that Dropbox is terrific, of course. No? Go and check it out now. One issue: files in your Public folder have a public URL, that you can send to other people. Unfortunately, directories do not. So how do you share a public directory full of files? Answer: create an index.html file and share that. Let’s say that your files end in “.txt” and reside in ~/Dropbox/Public/entrez. Do this: cd ~/Dropbox/Public/entrez echo "<ol>" > index.html for i in `ls *.txt`; do echo "<li><a href='$i'>$i</a></li>" >> index.html; done echo "</ol>" >> index.html Now you can share the link to the index.html, which when clicked will display a list of links to all the other files in the directory. Filed unde... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4152099 Tue, 09 Nov 2010 00:26:01 +0100 4152099 http://www.medworm.com/index.php?rid=4139330&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcool-technology-week-quest-gazelle As readers of my blog know, I'm passionate about mobile technology. I believe that iPhone/Android smartphones, iPod Touch, and the iPad, Playbook, Galaxy, and Streak will become the platforms for healthcare. Desktops with complex operating systems, antivirus, and heavy "thick client" applications will disappear.  Ray Ozzie's farewell message to Microsoft describes a post-PC world. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4139330 Fri, 05 Nov 2010 13:44:38 +0100 4139330 http://www.medworm.com/index.php?rid=4122011&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F10%2F30%2Ffindings-increasingly-novel-scientists-say%2F …was the tongue-in-cheek title of an image that I posted to Twitpic this week. It shows the usage of the word “novel” in PubMed article titles over time. As someone correctly pointed out at FriendFeed, it needs to be corrected for total publications per year. It was inspired by a couple of items that caught my attention. First, a question at BioStar with the self-explanatory title Locations of plots of quantities of publicly available biological data. Second, an item at FriendFeed musing on the (over?) use of the word “insight” in scientific publications. I’m sure that quite recently, I’ve read a letter to a journal which analysed the use of phrases such as “novel insights” in articles over time, but it’s currently eluding my sear... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4122011 Sat, 30 Oct 2010 05:41:17 +0100 4122011 http://www.medworm.com/index.php?rid=4098125&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fcool-technology-week-patienttouch Last week, I met with Patientsafe Solutions, a San Diego-based startup founded by serial entrepreneur James Sweeney. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4098125 Fri, 22 Oct 2010 13:37:59 +0100 4098125 http://www.medworm.com/index.php?rid=4082175&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fplanning-tomorrows-ehr After reading an article on the five key features of tomorrow's EHR, I wondered how the current EHR products are going to transition to meet the demands of healthcare providers and patients. In another five years, as EHR adoption grows, we are likely to see consumers wanting their patient data and tests electronically delivered in real time, coordination among their providers, and the ability to conduct many healthcare-related transactions online. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4082175 Tue, 19 Oct 2010 14:07:01 +0100 4082175 http://www.medworm.com/index.php?rid=4077353&cid=t_100098_112_f&fid=34971&url=http%3A%2F%2Fdoctorandpatient.blogspot.com%2F2010%2F10%2Fwhy-dont-indian-doctors-use-emrs.html Why do Indian doctors continue practising in exactly the same way their seniors did 40 years ago ?A major lacuna is the poor quality of medical records which most doctors keep. The medical record is the heart of clinical care - and yet it's extremely poorly maintained in Indian clinics today. The majority of doctors do not even bother to store and keep their patient's medical records - they just write down their opinion on their letterhead and hand it over to the patient. Usually, this is just a laundry list of tests the patients needs to do and a hand written illegible scrawled prescription - without even a mention made of the clinical findings or what the diagnostic impression is ! While it's good that the patient owns his own records, what happens if the patient forgets to get his recor... The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=4077353 Mon, 18 Oct 2010 02:05:00 +0100 4077353 http://www.medworm.com/index.php?rid=4031424&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FYXvzgVBdqOg%2F TweetDrew Conway has come up with a Data Science Venn Diagram. My favorite bit from the diagram is the “danger zone”. Drew positions the danger zone as follows Finally, a word on the hacking skills plus substantive expertise danger zone. This is where I place people who, “know enough to be dangerous,” and is the most problematic area of the diagram. In this area people who are perfectly capable of extracting and structuring data, likely related to a field they know quite a bit about, and probably even know enough R to run a linear regression and report the coefficients; but they lack any understanding of what those coefficients mean. It is from this part of the diagram that the phrase “lies, damned lies, and statistics” emanates, because either through ignorance or mali... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4031424 Tue, 05 Oct 2010 09:24:15 +0100 4031424 http://www.medworm.com/index.php?rid=4013300&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fmobile-results-reporting-solutions-help-physicians-stay-connected As physicians seek more efficient ways of accessing and managing clinical information, they are relying more and more on mobile technologies to increase patient safety and improve productivity. According to Manhattan Research, the number of physicians who owned smartphones in 2009 was 64 percent, and that number is expected to reach 81 percent by 2012. And, of those physicians who own smartphones, a recent study by the Spyglass Consulting Group revealed that 94 percent are using the devices to communicate, manage personal and business workflows, and access medical information. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=4013300 Tue, 28 Sep 2010 20:52:57 +0100 4013300 http://www.medworm.com/index.php?rid=3999182&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F5yRMHgkwQ4o%2F TweetIlya Grigorik has a great set of slides up on slideshare from his recent talk at the 2010 Golden Gate Ruby conference. The talk called Intelligent Rudy + Machine Learning is the kind of presentation I absolutely love. He talks about the what, the why, the trends, and relevant tools. Over the past few years, I’ve become fascinated with machine learning. For the longest time, from my perspective, machine learning was something for academics to play around with models without significant real world utility. The availability of data and computing has changed that, and today I am a convert to the power of machine learning, and wish we pushed the envelope more, at least in the life sciences. Some of this change in opinion is due to the adoption of machine learning in non-academic sett... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3999182 Fri, 24 Sep 2010 07:54:22 +0100 3999182 http://www.medworm.com/index.php?rid=3999181&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F09%2F24%2Fconnecting-to-a-mongodb-database-from-r-using-java%2F It would be nice if there were an R package, along the lines of RMySQL, for MongoDB. For now there is not – so, how best to get data from a MongoDB database into R? One option is to retrieve JSON via the MongoDB REST interface and parse it using the rjson package. Assuming, for example, that you have retrieved your CiteULike collection in JSON format from this URL: http://www.citeulike.org/json/user/neils - and saved it to a database named citeulike in a collection named articles, you can fetch the first 5 articles into R like so: library(RCurl) library(rjson) db <- "http://localhost:28017/citeulike/articles/?limit=5" articles <- fromJSON(getURL(db)) articles$rows[[1]]$title # [1] "A computational genomics pipeline for prokaryotic sequencing projects" ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3999181 Fri, 24 Sep 2010 07:15:00 +0100 3999181 http://www.medworm.com/index.php?rid=3999183&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FGwgfG0LfCIA%2F Tweet Image by mndoci via Flickr Back in grad school, I was a fan of using multiple shorter trajectories to sample protein space and then using statistics and principle component analysis to try and identify appropriate states. In my case, with limited compute power, I liked to generate ensembles of structures and then use them as candidates for further analysis, often as starting points for longer trajectories and seeing if they converged at all. Later, I was also a fan of replica exchange techniques to try and get better sampling. In a nutshell, I’ve never been a fan of the single long trajectory. I found that approach to be inherently unscalable (is that a word?) while more distributed approaches seemed to be more efficient, and, definitely in my case, a better use of time and li... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3999183 Fri, 24 Sep 2010 06:20:17 +0100 3999183 http://www.medworm.com/index.php?rid=3983518&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FMlgMpip11p8%2F TweetI don’t often do posts that are essentially just a link, but James Hamilton has an update to his well known model of the cost of a data center. The post includes a spreadsheet you can play with if you are interested. Worth a read if you care about infrastructure, scale, and what goes into powering many of the services we leverage in our lives. As a long time hardware geek, this is perfect Sunday reading and spreadsheet fun Watch James discuss some of these numbers and recent data center innovations at the recent Velocity conference (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3983518 Sun, 19 Sep 2010 19:08:19 +0100 3983518 http://www.medworm.com/index.php?rid=3982087&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FCD6ILq6hA48%2F Greg Linden points us to a great paper (pdf) on machine learning by folks at Google that was presented at LADIS ’10 (I’d love to go some day) The presentation covers Sibyl, a “system for large scale machine learning” and about Parallel Boosting, an iterative approach that does well at predictions based on sparse data. The Boosting page says that the boosting approach is designed to work with semi-accurate rules of thumb (made me think of ligand pose scoring for some reason). As might be expected from a Google approach it is embarrassingly parallel and uses the following approach (image from the talk PDF) They also talk about how they leverage RAM, lots of cores and GFS (column store). Greg does a great job of covering some of those aspects. This method allows the ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3982087 Sun, 19 Sep 2010 03:28:12 +0100 3982087 http://www.medworm.com/index.php?rid=3965729&cid=t_100098_180_f&fid=38607&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fsuccessbeginstoday%2FBHWQ%2F%7E3%2FEdE4mPbS-rg%2F Meetings are a way of life for many people. If you work in the corporate world, it seems like they can fill up the majority of your schedule. While meetings can be useful, they can also be huge time wasters. Today I would like to share with you three helpful tools to get the most out of your meetings and get back to more productive work quickly. 1. Desktop Flowchart: Here is a simple little tool that you can carry in your pocket or purse that can help when brainstorming during meetings. Just print a few sheets of these cards and create your own flowchart right on your desk. Pass out some cards, record some ideas, and sort them in an organized format. This tool works great in small groups of 6 to 8 people. Just fill in the cards and use the arrows to create flow. The deluxe desktop flowcha... Success Begins Today blogs http://www.medworm.com/rss/comments.php?id=3965729 Mon, 13 Sep 2010 13:58:05 +0100 3965729 http://www.medworm.com/index.php?rid=3915214&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F86SazMZWEzg%2F Image via Wikipedia In the past I’ve written about Dan Reed’s post about a Ruby on Rails for HPC. Pan Hanrahan at Stanford has a similar article in the summer issue of Biomedical Computation Review. Dr. Hanrahan argues that in the age of multicore, grids and clouds, parallel computing is ubiquitous. This is, or at least should be, great news for computational scientists, both on the simulation side and the data-intensive side. But there is always a challenge, and that challenge has not changed in years. How do you think and code in parallel? When you’re a computational biologist, you don’t want to spend your time thinking about lower level primitives (locks, concurrency, distribution, etc), but rather about the actual problem you want to solve where parallelism m... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3915214 Sun, 29 Aug 2010 19:34:39 +0100 3915214 http://www.medworm.com/index.php?rid=3885499&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F20%2Fa-brief-introduction-to-apply-in-r%2F At any R Q&A site, you’ll frequently see an exchange like this one: Q: How can I use a loop to [...insert task here...] ? A: Don’t. Use one of the apply functions. So, what are these wondrous apply functions and how do they work? I think the best way to figure out anything in R is to learn by experimentation, using embarrassingly trivial data and functions. If you fire up your R console, type “??apply” and scroll down to the functions in the base package, you’ll see something like this: base::apply Apply Functions Over Array Margins base::by Apply a Function to a Data Frame Split by Factors base::eapply Apply a Function Over Values in an Environment base::lapply Apply a Function over a List or Vector base::mapply Apply a Fun... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3885499 Thu, 19 Aug 2010 14:08:37 +0100 3885499 http://www.medworm.com/index.php?rid=3872632&cid=t_100098_113_f&fid=34637&url=http%3A%2F%2Fgaggio.blogspirit.com%2Farchive%2F2010%2F08%2F16%2Fmy-relax-3d.html There is nothing more regenerating than a long sea vacation. But what we do as we are back to the office and find an overwhelming pile of email? A good recovery strategy from post-vacation stress is essential, and advanced technologies may help. For example, My Relax 3D is a mobile application that helps you relax while watching at stunning 3D landscapes of an exotic island. When you enter the application, you can choose between highly realistic 3d environments, depicting various island scenarios (i.e. a tropical forest, a sunset) During the experience, a voiceover provides instructions to relieve from stress and develop positive emotions. The application is highly configurable: it can be experienced with or without 3D glasses (but I strongly recommend this option to enhance your feeling o... Positive Technology Journal blogs http://www.medworm.com/rss/comments.php?id=3872632 Mon, 16 Aug 2010 16:07:53 +0100 3872632 http://www.medworm.com/index.php?rid=3868803&cid=t_100098_112_f&fid=34971&url=http%3A%2F%2Fdoctorandpatient.blogspot.com%2F2010%2F08%2Fpatient-safety-seminar-by-dr-nikhil.html This is a guest post from Mr Aditya Patkar, Marketing Director, Plus91A few Sundays ago , I was privileged to be invited by Dr. Nikhil Datar, a pre-eminent gynecologist and medico-legal expert to witness his premier talk on Patient Safety. It was hosted by IMA Dombivali and over 40 doctors turned up to hear Dr. Datar’s talk. Dr. Datar had recently returned from UK where he attended a program organized by WHO on Patient Safety. I was there because Plus91 Technologies believes in making patient centric software solutions which don’t just automate the clinic or hospital , but also improve quality and service.The doctors quickly realized that they need to reflect and close loopholes in their own practice, so that they could ensure patient safety. Sometimes we are so focused on the trees, t... The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=3868803 Sun, 15 Aug 2010 14:17:00 +0100 3868803 http://www.medworm.com/index.php?rid=3845239&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FShGFWOdSkgM%2F Image of Matt Wood I’ve had the luxury of working in some very interesting areas; large scale protein structure prediction, physics-based approaches to drug discovery, data management for all kinds of molecular profiling data, and high-scale distributed infrastructure. I also have had the fortune of meeting some of the brightest people in the world at their craft over the years. In particular, over the past couple of years, I’ve met or observed some exceptionally bright people at the forefront of information retrieval and data mining. While there is a lot of naive, follow the latest trend, activity, there is also a lot of excitement. The web produces a lot of data, and many smart folks are trying to make sense of all that data. I am obviously biased, and can never really sto... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3845239 Sun, 08 Aug 2010 18:29:47 +0100 3845239 http://www.medworm.com/index.php?rid=3831510&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FG_G0HuH9XlU%2F It’s been two years since I first wrote about Foldit. By now you’re read all about how Foldit was used to solve structures, probably a first for game play. Does this mean that computation sucks? Not really. Folding is a hard problem, and no method out there really does a good job because our functions aren’t that good, but they are good at generating candidates. It just so happens that human beings are pretty good at taking those candidates and identifying good structures. This is not that surprising if you’ve been doing protein modeling for a long time. In fact, it would be interesting to combine game mechanics with some expertise and possibly some new interaction technologies (haptic feedback, touchpads, Kinect, etc). A good structural biologist can usually identi... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3831510 Sat, 07 Aug 2010 04:46:20 +0100 3831510 http://www.medworm.com/index.php?rid=3831417&cid=t_100098_112_f&fid=34971&url=http%3A%2F%2Fdoctorandpatient.blogspot.com%2F2010%2F08%2Fhow-medical-software-can-help-to.html This is a guest post from Mr Aditya Patkar, Marketing Director, Plus91.Patient Safety is a vital aspect of healthcare. Medical errors can lead to deaths and medical tragedies which are preventable , leading to heartburn and losses for all doctors and patients . In any industry, software is used to improve efficiency and accuracy. I am going to highlight some basic examples as to how medical software ( electronic medical records, EMR and practice management software, PMS) can be used to improve patient safety.1. Prescriptions and Medications: The commonest errors occur when doctors write prescriptions on paper and the patient or the chemist misreads the prescription. This is a common occurrence and a printed prescription generated from software with prepopulated Drug Data is the safest bet ... The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=3831417 Fri, 06 Aug 2010 18:18:00 +0100 3831417 http://www.medworm.com/index.php?rid=3802590&cid=t_100098_150_f&fid=35777&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FPharmalot%2F%7E3%2F2pcvgNkqy-U%2F Hello, everyone. A spot of rain is falling here on the Pharmalot corporate campus today. Nonetheless, our spirits remain sunny. Why? We are compelled to offer our periodic reminder, courtesy of the Morning Mayor: ‘Every brand new day should be unwrapped like a precious gift.’ So go ahead and tug on the ribbon. Meanwhile, please join us for a cup of stimulation as we scan the news of the world. Have a great day… Sanofi-Aventis To Bid $18 Billion For Genzyme (Bloomberg News) FDA Considers Changes To REMS Safeguards (Reuters) Lilly Dumps Amazon Web Services Over Legal Struggle (SearchCloudComputing) Sanofi-Aventis Lawsuit Over Zimulti Is Reinstated (Bloomberg News) Fewer ABPI Complaints In 2009, But More Appeals (PharmaTimes) Lilly Loses Appeal In Gemzar Patent Case (Dow Jon... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=3802590 Thu, 29 Jul 2010 11:24:11 +0100 3802590 http://www.medworm.com/index.php?rid=3721904&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJZKS2_mfuKI%2F Staying on my massive data processing theme here is a more practical post. In the world of large scale distributed processing, the original MapReduce paper will probably hold the most important position. Hadoop remains the most well known of all the MapReduce implementations, and is now a proven, battle-tested commodity. Tom White’s book is a great place to start if you have an interest in the framework itself, but the book I wanted to point out was Jimmy Lin’s book on Data-Intensive Text Processing with MapReduce (there is a pre-production PDF of the book from the homepage)  and it’s a great dive into algorithm design. The book talks about general algo design, indexing, graphs and a fabulous section on expectation maximization that is a must read for bioinformaticians w... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3721904 Sat, 03 Jul 2010 05:21:03 +0100 3721904 http://www.medworm.com/index.php?rid=3718624&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F02%2Fhow-many-monotypic-genera%2F During all the recent discussion around Neandertals and modern humans, it’s often pointed out that Homo sapiens is the sole extant representative of the genus Homo. I began to wonder “how unusual is this?” in a FriendFeed comment thread. What resources exist that could help us to answer this question? Genera that contain only one species are termed monotypic. Wikipedia even has a category page for this topic but their lists are limited, since Wikipedia is not a comprehensive taxonomy resource. Taxonomy is not my specialty but once in a while, I enjoy challenging myself with unfamiliar resources and data types. I figured initially that we could get some way towards an answer using BioSQL and the NCBI taxonomy database. As it turned out I was completely wrong, but it was an... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3718624 Fri, 02 Jul 2010 02:56:59 +0100 3718624 http://www.medworm.com/index.php?rid=3714365&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FCGWzRowuY50%2F I missed the talk, but at this week’s Hadoop Summit, Yahoo talked about Oozie, their workflow engine for Hadoop. Oozie is open source, and allows you to manage jobs between HDFS, Pig, and MapReduce. Oozie looks very interesting indeed. Workflows are arranged in a Direct Acyclic Graph, and you can make decisions, fork and join nodes, etc. The kind of workflow system that could make some bioinformatics pipelines very interesting to implement. The figure on the Oozie design page suggests one possible workflow Related articles by Zemanta 5 years later, Hadoop has matured (developer.yahoo.net) Yahoo adds security and workflow management to Hadoop (infoworld.com) (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3714365 Thu, 01 Jul 2010 06:26:31 +0100 3714365 http://www.medworm.com/index.php?rid=3714366&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FAn11TA9gOs8%2F Facebook 36 PB of uncompressed data 2250 machines 23,000 cores 32 GB of RAM per machine processing 80-90TB/day Yahoo 70 PB of data in HDFS 170 PB spread across the globe 34000 servers Processing 3 PB per day 120 TB flow through Hadoop every day Twitter 7 TB/day into HDFS LinkedIn 120 Billion relationships 82 Hadoop jobs daily (IIRC) 16 TB of intermedia data 2 engineers These are just some examples from Hadoop Summit. Many of these are production systems, others research systems. Also discussed were massive graphs (trillions of edges), insights from TBs of data ingested daily, etc. All held by a common thread, the Hadoop ecosystem (Hadoop is a lot more now than just an implementation of MapReduce). The next time I hear life science people complain about data volumes, shared storage, etc, I ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3714366 Wed, 30 Jun 2010 14:29:23 +0100 3714366 http://www.medworm.com/index.php?rid=3687300&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FSzJ8NYXeI7E%2F Image via Wikipedia Data has been in the news again lately. It’s a data-centric world, and it seems we can’t quite enough. Whether it’s the Cornucopia of Corpora at The Infochimps or all the patent data that Google just unleashed, or the Guardian Open Platform or the 1000 genomes project (on Amazon S3). It’s pretty clear that data is sexy, and to some degree overhyped (it’s not quite as simple as Data –> WIN!!!), but I, and others, clearly believe that data is important, and more, easier access to data can only be a good thing. Data is a constant theme on bbgm, but there’s something I am beginning to realize more clearly. It’s not about the specific implementations or technology choices we make. Those are important, but data science is ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3687300 Wed, 23 Jun 2010 06:12:44 +0100 3687300 http://www.medworm.com/index.php?rid=3666136&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FvF65L8B2vA0%2F I talk about some of these topics as part of my day job, but continue to be fascinated by what goes into computing at scale as I learn new things every day. On the flight from SeaTac to LAX late last evening, I jumped into Papers and re-read a great whitepaper (or should we call it a mini-book) on warehouse-scale computing. If you are interested in massive scale, data center design, etc, this is a great primer. Given that a couple of years ago, even my knowledge of these matters was limited, I am pretty sure the average life science type has limited knowledge of how datacenters are built and decisions are made at scale. This would be a great place to start. If you’re a physical chemist like me, you’re likely to find some of the thermodynamics of datacenter design quite fascinat... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3666136 Wed, 16 Jun 2010 07:35:19 +0100 3666136 http://www.medworm.com/index.php?rid=3652584&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F06%2F11%2Ffirst-cautious-steps-with-cuda%2F I recently obtained an account on our GPU cluster, so I thought I should get my head around some of the technology that drives GPU computing. Put simply, GPUs can be used to perform calculations and since there are many processors on a GPU, this can lead to quite substantial speed increases as compared with CPUs. NVIDIA are leading the way and they provide libraries and software tools for people interested in this field. Development is typically performed using C, C++ or Fortran. I’m not a compiled languages guy – I could just about manage a hello world in C – so I’m relying on tools built by other people, such as R gputools. Step 1 is to download and install the required libraries, toolkit and possibly, drivers. I ran into a couple of minor problems on my machine, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3652584 Fri, 11 Jun 2010 06:00:14 +0100 3652584 http://www.medworm.com/index.php?rid=3621888&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FTAX0P2wLFkc%2F Image via Wikipedia One of the questions my colleagues often ask me is why the bioinformatics universe has not made more use of Hadoop and similar techniques. Yes, our data sets are smaller (but they are growing at a rapid rate), yes, we have a lot of legacy code and our data changes a lot, but those are not real reasons in my mind, certainly not in the minds of those for whom six months is an eternity. These questions resurfaced as I went through Jake Hofman’s presentation at ICWSM 2010. On slide 21 he light heartedly talks about Hadoop, stating that the presentation might be boring to those who know how to install and use Hadoop and (and this is the part that caught my attention) implement distributed solutions for parsing and manipulating large text collections clustering coef... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3621888 Wed, 02 Jun 2010 05:00:15 +0100 3621888 http://www.medworm.com/index.php?rid=3618028&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fznfjh3vcWoA%2F The BBC has a great graphic on the Top 500 supercomputers. You can change around various parameters, but I found the following one on OS support telling Image source: BBC. Click here for full size (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3618028 Mon, 31 May 2010 19:35:54 +0100 3618028 http://www.medworm.com/index.php?rid=3614647&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FyuHSfQSn-5w%2F Doug Eadline has a really interesting article up on Disposable HPC, where he talks about how to mix scale with failure. In the past two years, I’ve really come to appreciate the concept of computing as a fungible commodity, but to live in this world you have to first realize that in a commodity world failure happens in all kinds of ways, for all kinds of reasons. Once you accept that, you can design appropriately. This is also a world of loosely coupled applications, or systems that understand that components could go away. One of the concepts that Doug talks about is Recovery Oriented Computing (ROC), which I first became aware of via James Hamilton. The core concept in ROC is that unanticipated failures are inevitable, and that human errors account for a large portion of all system... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3614647 Mon, 31 May 2010 01:27:07 +0100 3614647 http://www.medworm.com/index.php?rid=3592356&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F24%2Fif-you-must-send-me-an-excel-spreadsheet%2F …please, try to follow these simple guidelines. 1. Don’t bother to format the cells Where possible, I will not open your spreadsheet in a spreadsheet application. If I do, it will be only to marvel at the horror, then export it as rapidly as possible to a delimited text file. I do not care about the font, the font size or the font weight. I do not care whether there are grid lines around the cells. I especially do not care about cells which you have highlighted using some arbitrary (and unexplained) colour scheme. 2. No multiple tables If you include multiple “tables” on one sheet, separated by blank rows, there is a good chance that I will not notice them. If you include multiple tables on multiple “sheets”, there is an excellent chance that I will not ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3592356 Mon, 24 May 2010 06:33:57 +0100 3592356 http://www.medworm.com/index.php?rid=3592357&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F5tbjIuE_kis%2F via HPC in the cloud (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3592357 Sun, 23 May 2010 19:47:02 +0100 3592357 http://www.medworm.com/index.php?rid=3573865&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F18%2Fdata-management-its-funny-because-its-true%2F Please read My Data Management Plan – a satire Have a good giggle Ask yourself if anything sounds familiar If you answered yes to (3), do something about it That is all. Filed under: bioinformatics, blogroll, computing, programming Tagged: best practice, data management, humour, satire (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3573865 Tue, 18 May 2010 01:52:43 +0100 3573865 http://www.medworm.com/index.php?rid=3564049&cid=t_100098_112_f&fid=34971&url=http%3A%2F%2Fdoctorandpatient.blogspot.com%2F2010%2F05%2Fas-doctor-i-want-to-use-technology-to.html This is a guest post from Mr Aditya Patkar, Sales Director, Plus91, in which I am an angel investor.As we improve our software products and work with more doctors, we are learning a lot about what doctors in India want from information technology . How do Indian Doctors view IT as an enabler ? In theory, one would expect doctors to want to use IT for the following applications. 1. Computer Based Medical Records (EMR)2. Clinical Information Sharing Networks3. Clinical Decision Support4. Administrative Functions – Accounts and Patient Profile Management5. Computer Generated Prescriptions6. Better Patient Communication and CareHowever, what the practicing doctor wants in real life is quite different ! So what does the typical doctor’s list look like?1. Accounts and (Mis)-ManagementIndian ... The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=3564049 Fri, 14 May 2010 10:48:00 +0100 3564049 http://www.medworm.com/index.php?rid=3556202&cid=t_100098_113_f&fid=38236&url=http%3A%2F%2Fwww.healthcareitnews.com%2Fblog%2Fturning-cloud-hipaa-5010-and-icd-10-compliance Distant thunder rumbles across the HIPAA 5010 and ICD-10 horizon. That's the sound of cloud computing services gliding toward healthcare organizations. Cloud computing has already caught on in other facets of healthcare IT – and as providers and payers prepare to meet the pending mandates, hosted services could prove a viable option. (Source: Healthcare IT News Blog) Healthcare IT News Blog blogs http://www.medworm.com/rss/comments.php?id=3556202 Wed, 12 May 2010 13:07:42 +0100 3556202 http://www.medworm.com/index.php?rid=3556282&cid=t_100098_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FOX2IN5IiNdM%2F I recently wondered if there would be a time that scientific data APIs would get the kind of developer excitement that the Twitter API gets. To some extent that is wishful thinking. After all the type of data you get via Twitter and the type of data you get from next-gen sequencing are quite different and require a different level of expertise and understanding. But I do believe that smart developers especially those with a data mining bent can learn enough biology to really help and extend the field. I’ve been in enough meetings recently where there has been quite a bit if contention of roles in the life sciences. Some of it is semantics, but a lot of it is real. We have algorithm developers, bioinformaticians, biologists, software developers and perhaps roles that I am forgetting,... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3556282 Tue, 11 May 2010 22:33:50 +0100 3556282 http://www.medworm.com/index.php?rid=3552477&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F11%2Fbeware-of-rogue-header-files-bioconductor-installation%2F Just a short note concerning a “gotcha”. As I have many times before, I opened an R console on my newly-upgraded (to lucid 10.04) Ubuntu machine, typed source(“http://bioconductor.org/biocLite.R”) and began a Bioconductor install with biocLite(). Only this time, I saw this: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so': /home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so: undefined symbol: egzread ERROR: loading failed * removing ‘/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio’ A quick email to the Bioconductor mailing list put me in touch with the very helpful Martin Morgan, who suggested that I check my zlib libraries. Sure enough, ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3552477 Tue, 11 May 2010 06:18:18 +0100 3552477 http://www.medworm.com/index.php?rid=3538333&cid=t_100098_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F05%2F06%2Fmongodb-and-ubuntu-10-04%2F Fans of MongoDB and Ubuntu, rejoice. Installation just got easier, with the appearance of mongodb in the Ubuntu repositories. However – the latest version in lucid is 1.2.2, whereas you want the very latest, 1.4.2. All the instructions are here. As usual, it’s just a case of adding a line to your sources list, importing a GPG key and then: sudo apt-get update sudo apt-get install mongodb-stable Configuration lives in /etc/mongodb.conf, databases live in /var/lib/mongodb, logging goes to /var/log/mongodb/*.log. Filed under: computing, linux Tagged: 10.04, databases, lucid, mongodb, ubuntu (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3538333 Thu, 06 May 2010 05:38:40 +0100 3538333 http://www.medworm.com/index.php?rid=3526896&cid=t_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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_100098_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=2712294&cid=t_100098_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_100098_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