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 'informatics'. Sat, 03 Sep 2011 01:47:31 +0100 http://www.medworm.com/index.php?rid=5181957&cid=t_92073_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2F_VlWsGVP6dk%2F Normally this time of year, I’m making plans to attend the many fall conferences in health IT and related industries. This year, my decisions are harder. You see, it seems like everyone decided to schedule their events during the last week of October: AMIA 2011, Oct. 23-26, Washington MGMA Annual Conference, Oct. 23-26, Las Vegas TEDMED 2011 Oct. 25-28, San Diego CHIME11 Fall CIO Forum, Oct. 26-28, Austin, Texas Just for kicks, I’m scheduled to participate in the Institute for Health Technology Transformation’s Health IT Summit, Nov. 2-3 in Beverly Hills, Calif. All are worthwhile, and all will be great places to find relevant stories for this blog and my various media clients. It probably makes most sense to go west, hitting MGMA and TEDMED, then spending the weekend in ... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=5181957 Thu, 01 Sep 2011 16:47:10 +0100 5181957 http://www.medworm.com/index.php?rid=5169589&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FrkCHFKSkWUQ%2Fmedgadget-interview-robert-oschler-robotic-telepresence-developer.html Robert Oschler is a robotics enthusiast with a special interest in telepresence.  He has been developing his own software for years, but the latest iteration of his Robodance client brings together the Rovio robot and EPOC’s EEG-monitoring device.  We often report on the developments of huge companies in the medical technology field, so we thought it would be a good idea to take a look at some of the smaller-scale, independent developers who are exploring applications of human-technology interfaces that could one day be translated into health care applications.  We had a chance to ask Robert a couple questions, but he did want to make sure we made it known that he is not a physician and that the comments below are merely speculation. Medgadget. : How robust is the EPOC’s int... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5169589 Sat, 27 Aug 2011 15:13:06 +0100 5169589 http://www.medworm.com/index.php?rid=5139929&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FpYuKCjkgMkI%2Fvitreaview-universal-medical-image-viewer-gets-u-s-green-light.html Vital Images, a division of Toshiba Medical Systems, won FDA 510(k) approval of its VitreaView universal medical image viewer. The software, which allows for browsing through any DICOM and non-DICOM compliant images, runs via a web browser, and so does not require any software installs on client computers and will operate on any decent laptop, tablet, or desktop. VitreaView utilizes next generation technology for image distribution through a zero-footprint and zero download viewing solution. Users accessing VitreaView can use Web-enabled devices, including Windows® or Mac-based systems, for review of DICOM and non-DICOM medical images. This gives clinicians unrestricted access through the EMR, EHR or HIE to all patient imaging. Additionally, IT administrators can leverage virtualization f... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5139929 Wed, 17 Aug 2011 18:01:13 +0100 5139929 http://www.medworm.com/index.php?rid=5125824&cid=t_92073_113_f&fid=34625&url=http%3A%2F%2Ftraffic.libsyn.com%2Fnversel%2FVi_Shaffer_AMDIS_2011.mp3 Back in June, I covered the Wisconsin Technology Network’s Digital Healthcare Conference in Madison. That conference featured a panel with Vi Shaffer, research vice president and industry services director for healthcare providers at Gartner, Judy Murphy, vice president of information services at Aurora Health Care in Milwaukee, and Epic Systems CEO Judy Faulkner, based in nearby Verona, Wis. The panel discussed the question, “Is meaningful use a floor or a ceiling?” as I reported for WTN News. The conference also featured several sessions on how business intelligence and health information exchange can support Accountable Care Organizations. A month later, I saw Shaffer again at AMDIS Physician-Computer Connection meeting in Ojai, Calif. There, she presented preliminary ... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=5125824 Fri, 12 Aug 2011 17:24:05 +0100 5125824 http://www.medworm.com/index.php?rid=5118734&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2F7ZoFm-D13ro%2Fdigitial-dog-tags-for-your-personal-health-records.html Asahi Kasei, a Japanese technology company, has just developed a small RFID tag (pictured) for storing personal health records. The device allows clinicians and emergency response personnel to instantly access a patient’s health records using a phone or laptop.The tag incorporates Sony’s FeliCa smart card technology as it is currently compatible with a  large number of Japanese devices which incorporate FeliCa card readers. In an emergency or clinical setting, paramedics or clinicians can tap the tag against compatible equipment to view the medical data of its owner in just a few seconds. Asahi Kasei says that a patient’s entire medical history can be viewed. If the clinician needs to view larger data files, the tag can provide links to the data which is stored on extern... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5118734 Thu, 11 Aug 2011 18:16:37 +0100 5118734 http://www.medworm.com/index.php?rid=5078062&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FcrtSkbJCY78%2F This has been all over the web today, just thought I’d pass it along. DrChrono is an EMR iPad app from DrChrono, Inc. that has generated a lot of buzz recently.  Any practitioner who uses it in... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=5078062 Fri, 29 Jul 2011 03:16:41 +0100 5078062 http://www.medworm.com/index.php?rid=5051263&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F07%2Fa-different-paradigm-for-analyzing-the-competition-between-cerner-and-epic.html In a recent note, I discussed the competition between the Cerner and Epic EMRs and quoted another blog, Chilmark Research, to the effect that Cerner was moving in new strategic direction, emphasizing a network of services to provide communities of care (see: Cerner Fights Back in the EMR Market: A Community Network of Services + PHR). Such an approach is sometimes referred to as the development of a care coordination platform. I concluded that Epic's approach closely coincided with the business model currently favored by hospital executives and would probably continue to succeed in the market. Vince Kuraitis responded to my note with a comment that included a link to a lecture he had recently delivered titled Platform Wars (see: Platform Wars). The presentation can also be accessed at ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=5051263 Mon, 18 Jul 2011 13:43:40 +0100 5051263 http://www.medworm.com/index.php?rid=5036308&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2Fy984u9nrXdU%2Fclearpractice-launches-cloud-based-medical-ecosystem.html We’ve covered a number of EMR solutions here at Medgadget, but ClearPractice is attempting to go one step beyond most other options with its new Eden software solution. Eden combines the Nimble iPad app with a practice management solution which can manage billing, scheduling, and prescribing. Eden stores all of its data in ClearPractice’s cloud servers, and includes iPhone, Mac, and PC applications, so doctors can access patient data from anywhere. From the press release: The Eden practice management and EMR solution includes all the clinical, financial, and administrative features and functions physicians need to operate their practice in a cloud-based environment, eliminating the need for expensive on-premise hardware or software. Physicians and medical office staff can access the so... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5036308 Fri, 15 Jul 2011 17:03:50 +0100 5036308 http://www.medworm.com/index.php?rid=5028524&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2Fi3ym5nCbKuQ%2Fpanasonics-new-toughbook-h2-and-toughbook-tablet.html Panasonic has released a new rugged notebook in its Toughbook line, the H2. The Windows 7 machine is not only designed for mobile and demanding applications common in clinical care, but it can also withstand wear and tear that is inevitable in a busy hospital environment, such as being dropped or having liquids splashed on. The H2 has no fan vent through which things can enter, is powered by two hot swappable batteries for zero downtime, and has a screen that will look good even in direct sunlight, among other features. Additionally, Panasonic is promising to release later this year a Toughbook tablet powered by Android that will also have a screen good for working under the sun (think paramedics), rugged construction, and a battery life that should last a full work shift. More about the H... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5028524 Thu, 14 Jul 2011 17:24:45 +0100 5028524 http://www.medworm.com/index.php?rid=5028537&cid=t_92073_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2FEz9y6jiX7Dc%2F I’m getting ready to head west for, among other things, the annual AMDIS Physician-Computer Connection in Ojai, Calif., a high-level gathering of chief medical information officers. After years of fighting for a seat at the table, CMIOs now are being held up as a model, at least overseas. Specifically, my friends at E-Health Insider in the UK have embarked on a mission to have every NHS hospital hire a chief clinical information officer, the British equivalent of the CMIO. Read more about the British perspective on the American CMIO here. Related posts:Google’s health plans, and more on CMIOs Podcast: Dr. Bill Bria on CMIOs and medical informatics England learns from America (Source: Neil Versel's Healthcare IT Blog) Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=5028537 Sun, 10 Jul 2011 15:55:11 +0100 5028537 http://www.medworm.com/index.php?rid=5008352&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2Fxqi-hvs8Lng%2Fopenpcr-do-it-yourself-open-source-pcr-kit-now-shipping.html The folks at OpenPCR project have just announced they have started shipping the first batch of OpenPCR kits for your at-home DNA replication pleasure. The OpenPCR is a computer controlled 16 well PCR machine for the lab bench or a workshop/garage, with its own built-in screen. A DIY Xerox machine for DNA built mostly with off the shelf components and free schematics, which does thermal cycling as well as boiling, cooling, and freezing (4C) samples. From the first prototype, development of the OpenPCR took only 14 months, funded through Kickstarter with 158 people bringing in a total of $12,121. It costs $512 (compared to $3000 for a traditional PCR machine), but you will need to assemble it yourself from the package of parts using tools and instructions that are included. Some of the sugge... Medgadget blogs http://www.medworm.com/rss/comments.php?id=5008352 Fri, 08 Jul 2011 17:00:25 +0100 5008352 http://www.medworm.com/index.php?rid=4975975&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FW36g4JxeEX0%2Fmeducation-a-multi-lingual-drug-regiment-app-wins-harvard-challenge.html Children’s Hospital Boston and Harvard Med School just announced the winner of their “SMART” Platform Apps Challenge, a contest of web applications that take advantage of data within electronic medical records. Meducation, made by Polyglot Systems, is a simple tool for clinicians and pharmacists to print out easily understood personal medication instructions, including a choice for those instructions to be in any one of twelve languages. There are also demo videos available when referencing something a little more complicated than oral pills, such as asthma inhalers. Some features of the app from the product page: generates a printable CMI sheet containing both the SIG (instructions for use) and a medication-specific drug monograph for each medicine; provides such information at... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4975975 Tue, 28 Jun 2011 16:59:08 +0100 4975975 http://www.medworm.com/index.php?rid=4902616&cid=t_92073_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=4893602&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2F6WhC8LaENd0%2Fbodymaps-a-3-d-anatomical-atlas.html We last reported on BodyMaps when it was still in Beta, and it has now been officially released.  In case you missed that post, BodyMaps is a flash-based interactive anatomic atlas.  It is searchable via text or by just clicking on various parts of the body, a sort of Google Maps of human anatomy (incidentally, Google is working on Google Body, a similar project). Designed primarily for consumer education, it is a collaborative effort of GE HealthyImagination and HealthLine networks, a consumer health-information company. In addition to providing patients with the ability to learn more about their anatomy, the site is rife with links to videos about common maladies affecting the body part that is selected (and, of course, ads for products to fix what ails that organ).   While the resolu... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4893602 Thu, 02 Jun 2011 16:41:22 +0100 4893602 http://www.medworm.com/index.php?rid=4862656&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FAryUj4DbGgs%2Fibm-watson-shows-off-its-medical-knowledge.html IBM’s Watson, the supercomputer known for handily beating human contestants on Jeopardy! a few months ago, started to show off its more practical skills medical knowledge. It recently gave a demonstration to the Associated Press. According to the AP, Watson was gradually given information about a fictional patient with an eye problem. As more clues were unveiled — blurred vision, family history of arthritis, Connecticut residence — Watson’s suggested diagnoses evolved from uveitis to Behcet’s disease to Lyme disease. It gave the final diagnosis a 73 percent confidence rating. The medical version of Watson was trained with medical textbooks and journals, electronic health records, and sample questions from medical students. However, unlike Jeopardy!, where Watson was r... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4862656 Tue, 24 May 2011 18:56:51 +0100 4862656 http://www.medworm.com/index.php?rid=4852965&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FCE17dHDXEc8%2Fpenrad-compass-breast-mri-computer-aided-visualization-and-analysis-software.html PenRad has unveiled its Compass breast MRI analysis software.  The package resides on a conventional PC and automatically processes images coming from the MRI for immediate review by the physician. Features from the product page: Image registration Subtractions Multiplanar reformatting MIPs Angiogenesis Maps and curves 3D Navigation from MIPs Customizable hanging layouts Dynamic thresholding and peak series adjustment One click image save as .jpg One click movie save as .wmv Volume and morphologic analysis Integration with PenRad MIS and PenView Software only – installed on any minimum spec. PC Announcement: PENRAD™ DEBUTS COMPASS, AN INNOVATIVE SOFTWARE SOLUTION FOR BREAST MRI, AT THE SOCIETY OF BREAST IMAGING CONFERENCE IN SAN ANTONIO, TX&#823... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4852965 Mon, 23 May 2011 17:36:39 +0100 4852965 http://www.medworm.com/index.php?rid=4841639&cid=t_92073_112_f&fid=34971&url=http%3A%2F%2Fblog.drmalpani.com%2F2011%2F05%2Fdrowning-in-too-much-health-information.html There's no question that it's important to be well informed if you are ill. Knowledge is power ( which is why you go to your doctor - he knows more about medicine than you do !)While not having enough information can result in poor care, today unearthing too much information has become a much bigger problem, thanks to google.Any one can search for any health topic on google and instantly come up with thousands of results. It's become very easy to search , but to find the relevant information is much harder. Making sense of these results is hard to do - and causes a lot of heartburn !Users get lost and confused and this often results in paralysis by analysis. In fact, after trying this a few times, many give up all together, thinking it's too complex and way above their heads and ability to... The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=4841639 Thu, 19 May 2011 03:17:00 +0100 4841639 http://www.medworm.com/index.php?rid=4841648&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FHDAK-yDk2xI%2Fbarcos-new-breast-tomosynthesis-monitor.html Barco has just received the first ever FDA approval for a computer monitor to be used for viewing breast tomosynthesis imagery.  Tomosynthesis involves sequential movie-like playback of images of the breast taken from different angles, so the monitor has to properly render each frame quickly and with precision. From the product page: RapidFrame ™: RapidFrame technology counteracts motion blur when scrolling through a stack of images due to a high pixel refresh rate. Per Pixel Uniformity™: PPU measures and adjusts the luminance of each pixel, making every pixel permanently DICOM compliant. SmoothGray™: SmoothGray generates ultra-precise representations of grayscale images and eliminates quantization artifacts, reducing the overall noise in the images. DuraLight Nova™: the DuraLig... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4841648 Wed, 18 May 2011 19:40:38 +0100 4841648 http://www.medworm.com/index.php?rid=4821173&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F05%2Fphysicians-and-the-two-screen-revolution.html In a recent note, I discussed the two-screen revolution that seems to be gaining traction (see: iPad Helping to Launch a "Two-Screen Revolution"). The basic idea is that many of us we will soon be operating with two screens, the large one being a TV or PC monitor and the small one being a tablet computer such as an iPad for simultaneously browsing the web. The large screen provides generalized, standard content and the smaller one provides customized, complementary information. I have been thinking about how this computing model relates to physicians and I think I can now describe how it may work in a hospital or large clinic. Consider the process that occurs when a physician accesses the electronic medical record of a patient using a computer monitor. He or she, using an iPad, c... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4821173 Fri, 13 May 2011 12:58:48 +0100 4821173 http://www.medworm.com/index.php?rid=4813390&cid=t_92073_112_f&fid=34971&url=http%3A%2F%2Fblog.drmalpani.com%2F2011%2F05%2Fhealthwise-patient-education-solution.html The Healthwise Patient Education Solution provides evidence-based patient instructions for virtually any moment in care. The meaningful health content includes instructions on how to prepare for upcoming procedures, after-care instructions, drug leaflets, and guidelines for when to call for help. And the patient instructions include “Go to Web” codes that directly link patients to more health information and interactive decision aids in the Healthwise® Knowledgebase, an online health encyclopedia. The Patient Information Education Trust is the Indian distributor for Healthwise ! (Source: The Patient's Doctor) The Patient's Doctor blogs http://www.medworm.com/rss/comments.php?id=4813390 Wed, 11 May 2011 12:14:00 +0100 4813390 http://www.medworm.com/index.php?rid=4820944&cid=t_92073_113_f&fid=22291&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FMedgadget%2F%7E3%2FOcgcQT4GAM0%2Fstudy_finds_that_iphone_app_can_make_accurate_stroke_diagnosis.html Researchers from the University of Calgary have shown that doctors can make a stroke diagnosis using an iPhone application just as accurately (and faster) than they can on a traditional computer. In a study recently published by Journal of Medical Internet Research, two neuro-radiologists looked at 120 consecutive noncontrast computed tomography (NCCT) scans and 70 computed tomography angiogram (CTA) head scans. One used a diagnostic workstation and the other using Calgary Scientific‘s ResolutionMD Mobile app. The study results showed that using the ResolutionMD app is between 94%-100% accurate in diagnosing acute stroke, compared to a medical workstation. In addition to accurately diagnosing a stroke, the app was also praised for its ability to handle a large number of images seamle... Medgadget blogs http://www.medworm.com/rss/comments.php?id=4820944 Tue, 10 May 2011 19:30:45 +0100 4820944 http://www.medworm.com/index.php?rid=4734111&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2F0PUl5FELmM4%2F Juggling work commitments, family life and writing can be tricky. However, new vigour and inspiration has been instilled with the arrival of some geeky new toys from Samson and Sanuk Australia. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4734111 Tue, 19 Apr 2011 03:37:17 +0100 4734111 http://www.medworm.com/index.php?rid=4724139&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FhmgKtaIscWE%2F Tweet In the life science software world, we are always trying to make software “easier to use by biologists”. Over the years, I’ve decided that means that the user interface and level of functionality should enable a biologist to ask the right questions and the workflow should fit their way of thinking and interrogation. Unfortunately, too often that ends up being interpreted as “let us make some form of GUI which is easy to use” without really thinking through that. At the same time, to do any sort of in depth analysis and drill downs you need a certain level of skill which no amount of “let’s make it easier to use” can solve. Which is why Mike Loukides’ post on Data Hand Tools made me smile. The post highlights some of the simple too... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4724139 Sun, 17 Apr 2011 17:42:34 +0100 4724139 http://www.medworm.com/index.php?rid=4684772&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F04%2Fwsome-types-of-cancer-more-prevalent-among-the-wealthier-australians.html Frequently, but now always, cancer strikes people in the lower socioeconomic groups. The development of cancer can be related to poverty or lifestyle issues including poor nutrition, smoking, alcohol abuse, obesity, and access to care. A recent article took a difference tack and discussed cancers that are more prevalent among the wealthy in Australia (see: Some cancers more prevalent in the wealthy), Below is an excerpt from it: A new report has shown that Australians living in wealthy areas are more likely to get breast, prostate and skin cancers than those living in poorer zones. The report from Australian Institute of Health and Welfare...also shows that those living in disadvantaged parts of the country are more likely to have bowel, cervical and lung cancers. Not so much with bowel ca... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4684772 Thu, 07 Apr 2011 15:23:52 +0100 4684772 http://www.medworm.com/index.php?rid=4684638&cid=t_92073_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=4670192&cid=t_92073_113_f&fid=34625&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FNeilVerselsHealthcareItBlog%2F%7E3%2F_hBCdv1Il8k%2F It’s time for another baseball season, and Health Wonk Review is ready to go. as with the Spring Training Edition two weeks ago, optimism reigns. (Host Jason Shafrin of the Healthcare Economist blog proves it by calling for the Milwaukee Brewers to win the World Series this year. I guess cheeseheads are still from the Green Bay Packers’ victory in the Super Bowl two months ago.) I didn’t make the starting lineup, but am an early choice from the bullpen for my “Slams on Berwick are getting pathetic” post. Curiously, Shafrin wades away from the controversy a bit by highlighting something said by a person I’m critiquing, namely that comparative effectiveness research “doesn’t work in the real world.” Not surprisingly, no post related to he... Neil Versel's Healthcare IT Blog blogs http://www.medworm.com/rss/comments.php?id=4670192 Fri, 01 Apr 2011 17:05:28 +0100 4670192 http://www.medworm.com/index.php?rid=4606058&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F03%2Fcameras-monitoring-traffic-lights-shown-to-save-lives.html It had never occurred to me before, but it makes perfect sense that cameras positioned at red lights to monitor traffic infractions can save lives (see: Red-Light Cameras Save Lives). Below is an excerpt from an article discussing this topic: A recent study by the Insurance Institute for Highway Safety has shown that red-light cameras saved 159 lives over a four-year period in the 14 large U.S. cities where the study took place. The scientists claimed that more than 800 traffic fatalities would have been prevented during the course of the study if the cameras had been deployed in all large U.S. cities. The scientists compared fatal car crash rates in U.S. cities with populations of at least 200,000 for two four-year periods: 1992 to 1996 and 2004 to 2008....In the 14 cities that used red-l... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4606058 Thu, 17 Mar 2011 19:56:51 +0100 4606058 http://www.medworm.com/index.php?rid=4577940&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2011%2F03%2F12%2Freport-from-amia-all-diseases-will-become-orphan%2F The first speaker I heard at the American Medical Informatics Joint Summit was Kenneth Buetow from the National Cancer Institute. In his typical provocative manner, he challenged the audience on the transition day from the Translational Bioinformatics to the Clinical Research Informatics Summits.  He began with promoting the P4 Medicine as the new model for healthcare: personalized, predictive, preemptive, participatory. Although throughout the conference little was articulated on the participatory aspects with one exception. More on that later. Buetow talked about defining cancer on the molecular level and the challenge of the exponential number of patients required to do genetic screening for a single disease. He referred to Pharma 3.0 from the Ernst and Young report on Progressions 20... eHealth blogs http://www.medworm.com/rss/comments.php?id=4577940 Sat, 12 Mar 2011 07:18:27 +0100 4577940 http://www.medworm.com/index.php?rid=4560389&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2011%2F03%2F07%2Famerican-medical-informatics-association-clinical-research-informatics-summit%2F Heading to San Francisco for this AMIA meeting. Looking forward to the opportunity to present from the podium and poster session. Topics include: Development and Sustainability of an EHR-based Chronic Kidney Disease Registry REDCap – Characterizing the Rapid Adoption at a large Academic Health Center Design of a Registry Management Tool for EMR Data Research Recruitment in Anesthesia Using EMR Data There will be many opportunities for networking. Hope to come home with lots of ideas. Hash tag is #TBICRI11 (Source: eHealth) eHealth blogs http://www.medworm.com/rss/comments.php?id=4560389 Tue, 08 Mar 2011 03:01:07 +0100 4560389 http://www.medworm.com/index.php?rid=4552124&cid=t_92073_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=4507388&cid=t_92073_113_f&fid=34634&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FEmrAndHipaa%2F%7E3%2Fdrgkja0ersI%2F As many of you know, EMR and HIPAA is a big time news company. We have a really fat budget and pay our reporters huge amounts of money to sit and smoke cigars while producing very little content of value. One of our biggest expenses here at HIMSS is in our investigative reporting department. Our motto is that if someone else breaks a story before us, then we spend the money to break them. Yes, we’re very serious about spending outrageous money breaking stories that no one else can break. After 3 years of investigation (and no government stimulus money), we’ve finally cracked the code on who’s behind the famous (and hilarious) Extormity EHR software. They’ve been very good about concealing their identity before their big HIMSS press conference in 312C, West Building.... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4507388 Tue, 22 Feb 2011 14:46:10 +0100 4507388 http://www.medworm.com/index.php?rid=4489893&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fi6AUw5G2950%2F Tweet Neil’s been on a roll lately. His latest post touches upon something that I have written about and believe in deeply. Two bits in particular stood out know the data sources, know the right tools and you can always sculpt a solution for your own situation. (It didn’t surprise me one bit that Matt Wood picked up on this as well) and Good web search skills are an essential part of the bioinformatics toolkit, but they don’t define the job. Real bioinformaticians write code. That we need to even say this is what you get from the Curse of Blast. We have too much of the data danger zone in life sciences, and bioinformatics ends up being diluted enough that people like me end up searching for alternative terms that highlight the informatician as data explorer, as data hack... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4489893 Fri, 18 Feb 2011 04:21:25 +0100 4489893 http://www.medworm.com/index.php?rid=4477981&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F61xj8hYcsnw%2F Tweet Lots of interesting discussion around the web on the rise of data-driven startups and product teams. Russell Jurney’s blog post on Analytic Product Teams has picked up a lot of press, and in general that is a topic that the LinkedIn SNA team talks about quite a bit. Bradford Cross has eloquently covered Research-driven startups and more recently, this comes up in a Dataspora article on mining big data What strikes me about this, especially light of Neil’s recent post on data scientists and my own past is that in some ways the social science space is going through a fascinating discovery about the value of data-driven products, something that some of the web giants have been doing for a long time. The difference now is that (a) there is an abundance of data, data sources ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4477981 Mon, 14 Feb 2011 14:32:43 +0100 4477981 http://www.medworm.com/index.php?rid=4460190&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F02%2Fthintroducing-the-eicu-what-is-it-and-why-is-it-now-being-introduced.html I recently stumbled upon a successful example of telemedicine about which I was unaware -- the enhanced intensive care unit (eICU). Provena Health, with six hospitals in Illinois, has a web page explaining the concept which I quote from below (see: eICU - enhanced ICU): Initially one of only a handful of health systems to implement eICU technology, the Provena eICU Connection is one of 43 eICUs of its kind in the country, which collectively monitor approximately 10 percent of ICU beds nation-wide and lead the way in innovative patient care....It's a revolutionary service that utilizes enhanced computer software and physiology monitoring technologies to get immediate critical care physician and nurse input about any change in a patient's condition....eICU technology adds to current ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4460190 Thu, 10 Feb 2011 13:02:49 +0100 4460190 http://www.medworm.com/index.php?rid=4450526&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F02%2Fontario-ges-omnyx-establish-digital-pathology-center-of-excellence.html GE has announced an agreement to establish its first Global Pathology Imaging Centre of Excellence in Toronto, Ontario. GE and its digital pathology joint venture, Omnyx, will invest $7.75M along with a $2.25M grant from the Health Technology Commercialization Program created by HTX (Health Technology Exchange) and funded by the Ontario Ministry of Research and Innovation. Planned collaborative research and development partnerships will bring an additional $7.2M, for a total investment of $17.2M over the next 3 years (see: GE and the Government of Ontario Establish First Global Digital Pathology Centre of Excellence to Improve Patient Care). Three facts were listed at end of the press release that provided some insight for me about why the Canadian government was interested in jump-startin... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4450526 Tue, 08 Feb 2011 13:19:14 +0100 4450526 http://www.medworm.com/index.php?rid=4419460&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fepic-employee-turnover-keeping-up-with-the-huge-number-of-new-contracts.html In a recent note, I quoted Mr. HIStalk describing how Epic manages its sales process (see: Some Details about the Epic Sales Force and Sales Process). In the same blog note that I linked to, he also cites the recent success of Epic in writing new EMR contracts (see: Monday Morning Update 1/24/11) Until 2009, Epic was making just 10-15 new sales a year and many of those were just for ambulatory or inpatient alone, but the percentage of enterprise sales has increased each year. In 2010, they supposedly made around 40 new sales .... Continuing on in this same vein regarding Epic staffing and personnel issues, Mr. HIStalk responds to a query for a reader, QPFC, about some sour grapes from ex-employees on the web (see: News 1/26/11): From QPFC: “Re: Epic. On Glassdoor.com, ex-employees have s... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4419460 Mon, 31 Jan 2011 12:58:51 +0100 4419460 http://www.medworm.com/index.php?rid=4389298&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F_wrgZ-dxajk%2F Tweet Danny Navarro has a great blog post on how and why sharing proteomics data is trickier than it seems. As informaticians we are quick to blame our experimental brethren about being protective of their data (although I think many computational types are very protective as well). Danny’s very valid point is that this is not as simple as just that. One of the core points he brings up is something I care about deeply, infrastructure. I won’t go into details about the various proteomics data sharing resources and their respective strengths and weaknesses. Read Danny’s post for that. What is telling is that there seems to be a trend in the community to try and come up with sets of standards, or a catch all repository, but limited agreement in what the right answer is. ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4389298 Sun, 23 Jan 2011 18:35:50 +0100 4389298 http://www.medworm.com/index.php?rid=4389299&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FpXVd9W04oME%2F Tweet Last night I was attended a rather interesting private event. I won’t talk about the event in detail since it was private, but it was a mix of life science folks and technologists, with the latter pushing the former to try and get a sense of scale and boundaries. The difference in mindset between engineers and scientists was so apparent at that time. While much of the discussion was centered around really hard biological and computational problems I was reminded that science is not just about solving really hard problems. Much of it is incremental, a result of access to new types of experiments and data and increased knowledge in the field. These days, one of the core challenges to this incremental form of discovery is that a number people are bound by storage, by computation... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4389299 Sun, 23 Jan 2011 06:01:55 +0100 4389299 http://www.medworm.com/index.php?rid=4372052&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2F06q9U-Q4HJk%2F aka Trauma Tribulation 008 A 26 year-old male was BIBA after falling off his stationary motorbike at a set of traffic lights. C-spine precautions were removed following palpation of his neck and assessment of his sphincter tone. Initially, his only complaint was pain to his right thumb, presumably from a hyperextension injury. However a detailed [...] (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4372052 Wed, 19 Jan 2011 00:00:30 +0100 4372052 http://www.medworm.com/index.php?rid=4361314&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fhealthy-days-per-month-as-a-measure.html A recent article about racial health disparities in the New York Times using CDC data was fascinating and I recommend it for anyone interested in general health issues (see: Broad Racial Disparities Seen in Americans’ Ills). To whet your interest, here are three short statements extracted from it: Babies born to black women are up to three times as likely to die in infancy as those born to women of other races. American Indians and Alaska Natives are twice as likely to die in car crashes as any other group. More than 80 percent of all suicides are committed by whites, but young American Indian adults have the highest suicide rates by far — 25 per 100,000 population at age 21, compared with 14 for whites, 10 for blacks and 8 for Asians and Hispanics. Compared with whites, blacks have d... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4361314 Tue, 18 Jan 2011 14:35:11 +0100 4361314 http://www.medworm.com/index.php?rid=4361315&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fis-meditech-dooomed-becasue-of-lack-of-robust-ambulatory-product.html Until about ten years ago, there was only minimal interest in IT support for ambulatory care. Successful EMR vendors such as that of Cerner were focused on inpatient care although their forward-looking "vision" statements always included ambulatory care. In terms of their major product focus, however, they were following the lead of the hospital executives who derived the bulk of their revenue from the inpatient side of the hospital. Many physicians shared this view at this time. Academic surgeons, for example, operated on mainly inpatients and then saw them as outpatients mainly to ensure that the surgical incisions were healing. All of this is now changing. Epic, for example, initially focused on IT support for ambulatory care. We all know how this has ended up (see: Why Does E... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4361315 Mon, 17 Jan 2011 15:19:55 +0100 4361315 http://www.medworm.com/index.php?rid=4343347&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Ftu.html I had previously heard about Google Goggles but do not have the app on my smartphone -- I don't have an Android phone. However, I may consider one in the future. It turns out that the app can perform a new trick that astonishes me (see: Android Google Goggles Adds Barcode Scanning, Sudoku Cheats). Below are the details: Google's latest version of Google Goggles is apparently powerful enough to beat a Sudoku champ at her own game....Google announced Goggles 1.3 client for Android, featuring instant barcode scanning and print ad recognition. And as an added bonus, Goggles 1.3 can also help you cheat on Sudoku. First released on Android phones in December 2009 and on iOS in October 2010, Google Goggles is a visual recognition app that allows users to photograph objects and receive rel... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4343347 Thu, 13 Jan 2011 12:48:54 +0100 4343347 http://www.medworm.com/index.php?rid=4338271&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fwfewer-hospital-admissions-for-health-failure-among-better-educated.html I have long been interested in the correlation between good health and level of education (see: Correlation of Sociodemographic Status with Personal Engagement in Cancer Screening Programs). Here's a quote from an article in the NYT that succinctly summarizes this issue (see: A Surprising Secret to a Long Life: Stay in School): James Smith, a health economist at the RAND Corporation, has heard a variety of hypotheses about what it takes to live a long life — money, lack of stress, a loving family, lots of friends....But what, he asks, is cause and what is effect? And how can they be disentangled? He is venturing, of course, into one of the prevailing mysteries of aging, the persistent differences seen in the life spans of large groups....But the questions for researchers like Dr. Smi... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4338271 Wed, 12 Jan 2011 14:29:39 +0100 4338271 http://www.medworm.com/index.php?rid=4331251&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fhow-valid-is-some-criticism-of-clinical-software.html Anecdotal information is defined as being based on personal experiences or, alternatively, on reports of individual cases rather than more rigorously acquired data. With regard to the selection of a new information system such as an LIS, it is nearly impossible to obtain detailed side-by-side comparisons of competing systems in the market. I personally pay no attention to the KLAS rankings (see: Mr. HIStalk Comments on KLAS). In order to make an informed decision when replacing an LIS, is it therefore necessary to perform a rigorous request-for-proposal (RFP) (see: More Ideas about Developing and Refining an RFP, Assessing the True Cost of Serving as a Beta Test Site for the Beaker LIS). It's also very important make a number of telephone calls to current users of the system. Mr. HISta... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4331251 Tue, 11 Jan 2011 13:51:34 +0100 4331251 http://www.medworm.com/index.php?rid=4318553&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2011%2F01%2Fcerner-lowering-lis-prices.html This article on Idaho hospital EMR projects describes Cerner, being implemented at North Canyon Medical Center for $2 million, as “an economical system that works well for smaller rural hospitals.” Syringa Hospital (a strangely satisfying hospital name) paid $1.3 million. What? The Cerner EMR as “an economical system that works well for smaller rural hospitals.” I, like Mr. HIStalk, was surprised by this description and had to think about the idea for a while. Then some of my thoughts started to come together. First of all, and as I noted in a previous note, Epic is winning most of the contracts for the highest-end hospital contracts, which was one of Cerner's sweet spots (see: Why Does Epic Keep Hammering Cerner? Mr. HIStalk's Opinion). Also, and as suggested in a previous... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4318553 Thu, 06 Jan 2011 14:19:00 +0100 4318553 http://www.medworm.com/index.php?rid=4295005&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F12%2Ftop-.html I tend to be a sucker for the various "top ten" lists and they are common at this time of year. I tend to always read them, mainly to see if I agree with the list. Hence my interest in the "top 11" technology innovations of the past ten years published by the IEEE (see: The top 11 technology innovations of the last 10 years, from the IEEE). IEEE is an organization that bills itself on its web site as "the world’s largest professional association dedicated to advancing technological innovation and excellence for the benefit of humanity." Why the top eleven? I suspect that there were some ties and controversy near the end of the list and they settled on eleven rather than ten. Here's their list: Smartphones. Social Networking. Voice over IP. LED Lighting... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4295005 Tue, 28 Dec 2010 14:46:39 +0100 4295005 http://www.medworm.com/index.php?rid=4225676&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F12%2Fmore-information-about-googles-chrome-os.html In a previous note, I began to address the Chrome browser/operating system (see: The Decline of Microsoft: The Clues Seem to Be Obvious). A recent NYT article begins to fill in some of the white space concerning this product (see: For Google, the Browser Does It All). Below is an excerpt from it: ....Chrome stores everything that people have on their computers — like documents, photos and e-mail — online, or in tech parlance, in the cloud. In Google’s vision of a world where all computers run on its Chrome OS, anyone can walk up to any computer with an Internet connection and gain access to all their information....It is all the more confusing because Google already has a Web browser named Chrome. And Google already has an operating system, called Android. Google says it will become ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4225676 Thu, 02 Dec 2010 20:42:46 +0100 4225676 http://www.medworm.com/index.php?rid=4214121&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FIGz3MSQO44U%2F Introducing Life in the Fast Lane's new searchable and sortable online Emergency Medicine and Critical Care Podcast Database (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4214121 Wed, 01 Dec 2010 05:14:20 +0100 4214121 http://www.medworm.com/index.php?rid=4207448&cid=t_92073_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=4206093&cid=t_92073_155_f&fid=38412&url=http%3A%2F%2Fpathlabmed.typepad.com%2Fsurgical_pathology_and_la%2F2010%2F11%2Flab-report-makeover.html Anyone read this month's issue of Wired (November 2010)? There is a fascinating article for us lab folks in which the author (Steven Leckart) tapped three designers to re-design the standard lab report.  First, let me say that the standard lab report design harkens back to the days of dot-matrix printers and green bar fanfold paper.  There seems to be little evolution since.  The lab reports from my lab invite more questions from clinicians and I field at least 3 calls per week just trying to cipher the results for the ordering physician!  Imagine a patient trying to make sense of their own lab results.  Actually, I can.  Every few months I receive a pdf by email from my dad or mom wondering what their lab results mean and if the "H" or &qu... The Daily Sign-Out blogs http://www.medworm.com/rss/comments.php?id=4206093 Fri, 26 Nov 2010 20:46:06 +0100 4206093 http://www.medworm.com/index.php?rid=4190391&cid=t_92073_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=4183562&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F11%2Fnew-malamoma-detection-device-narrowly-apporoved-by-the-fda.html MelaFind, a device designed for use by dermatologists for in-vivo detection of suspicious pigmented skin lesions, has been narrowly approved by an FDA advisory panel. Here is an excerpt from the article (see: Panel Splits over Skin Cancer Detection Device): An FDA advisory panel has voted 8-7, with one member abstaining, to recommend approval for an experimental skin cancer detection system called MelaFind. A vote so close generally is not considered an endorsement in the eyes of FDA officials, who have the final say in whether to approve the device. The FDA does not have to follow the advice of its advisory committees, but it often does. Some panelists on the [committee] were concerned that relying on a device to detect melanoma could lead to unnecessary biopsies, or worse: missed skin ca... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4183562 Fri, 19 Nov 2010 17:06:09 +0100 4183562 http://www.medworm.com/index.php?rid=4183255&cid=t_92073_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F11%2Finsurers-test-data-profiles-to-identify.html Stories like this one today at the WSJ disturb me.“Insurers Test Data Profiles to Identify Risky Clients”Wall Street JournalNov. 19, 2010From that story: Life insurers are testing an intensely personal new use for the vast dossiers of data being amassed about Americans: predicting people’s longevity. Insurers have long used blood and urine tests to assess people’s health—a costly process. Today, however, data-gathering companies have such extensive files on most U.S. consumers—online shopping details, catalog purchases, magazine subscriptions, leisure activities and information from social-networking sites—that some insurers are exploring whether data can reveal nearly as much about a person as a lab analysis of their bodily fluids. In one of the biggest tests, the U.S. arm o... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4183255 Fri, 19 Nov 2010 15:59:00 +0100 4183255 http://www.medworm.com/index.php?rid=4151938&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F11%2F08%2Femr-article-gets-positive-press%2F The article I coauthored in the Clinical Journal of the American Society of Nephrology, Development and Validation of an Electronic Health Record–Based Chronic Kidney Disease Registry,  received a nice press release from the American Society of Nephrology which was picked up by both medical and health IT news sources: Medscape: CKD Registry Could Help Physicians Improve Patient Care Healthcare IT News: EHR-based registry could transform chronic kidney disease care Healthcare Informatics: ??????Study: Kidney Disease Registry Could Help Patient Care Blogs: Science Centric: Health registry could transform chronic kidney disease care Drugs-Expert: Chronic Kidney Disease Care Could be Transformed by Health Registry I think that this registry is a model for others which utilize EMR data t... eHealth blogs http://www.medworm.com/rss/comments.php?id=4151938 Tue, 09 Nov 2010 04:01:39 +0100 4151938 http://www.medworm.com/index.php?rid=4151803&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FPzb-70upAEc%2F If you silence the alarm for any reason and there is subsequent oxygen supply failure within the next 2 minutes you will have no audible alarm. Unlike other ventilators on the market the Oxylog® 3000 cannot ventilate without an oxygen supply. This issue has been raised with Dräger but they have elected not to perform a software upgrade as they don’t see the need to offer a breakthrough alarm system for this potentially lethal fault... (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4151803 Tue, 09 Nov 2010 01:29:38 +0100 4151803 http://www.medworm.com/index.php?rid=4142924&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FQ4Z3IdCJ2QM%2F Tweet Ben Black has a great blog post on GigaOm on scale-driven database architecture. There are two key messages there that I would like reiterative in the context of modern biology. The first comes right at the beginning of the post Scale breaks everything. Scale even breaks your assumptions about how best to store and query data. Scale does not care about your personal engineering preferences, or about SQL vs. NoSQL. The demands of rapid growth and ever-higher expectations for availability, performance, and cost efficiency force you to re-evaluate and re-imagine what you need, what is possible, and how to best achieve your businessscientific goals. The second message comes in right at the end Lost in all the debates about SQL vs. NoSQL, ACID vs. BASE, CAP, and all the rest is simply ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4142924 Sat, 06 Nov 2010 18:41:39 +0100 4142924 http://www.medworm.com/index.php?rid=4142733&cid=t_92073_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F11%2Fon-amias-jan-2009-letter-to-office-of.html I was somewhat taken aback by the appearance of the article by Karsh et al. entitled "Health information technology: fallacies and sober realities" (covered at Healthcare Renewal here) in the Nov. 2010 Journal of the American Medical Informatics Association (JAMIA).I was taken aback since the article rains heavily on the academic memes of healthcare IT as a benign and deterministic solution to healthcare's ills, and of health IT-related adverse outcomes being mere "anecdotes."(It is ironic that my own mother recently fell victim to healthcare IT's supposed beneficence. It is accurate to say she was nearly killed via health IT-related cognitive disruptions and the resultant utter failure of medication reconciliation, and remains severely impaired nearly six months later.)My blog posting on ... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=4142733 Sat, 06 Nov 2010 14:01:00 +0100 4142733 http://www.medworm.com/index.php?rid=4139321&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F11%2F04%2Fpersonal-trifecta%2F One of the advantages of having a personal blog is not only expressing one’s opinions but also promoting accomplishments. I have been fortunate to have three in recent months: coauthorship on a major article on a disease registry from EMR data - Development and Validation of an Electronic Health Record–Based Chronic Kidney Disease Registry, Clinical Journal of the American Society of Nephrology, Nov. 2010. Press Release:Health Registry Could Transform Chronic Kidney Disease Care named in an NIH grant: Refinement and Enhancement of a Web-Based Risk Calculator Deployment System named a Fellow in the Health Information and Management Systems Society (HIMSS) Also, I became a fellow in the Group for Information Resources of the American Association of Medical Colleges this summer ... eHealth blogs http://www.medworm.com/rss/comments.php?id=4139321 Fri, 05 Nov 2010 02:34:27 +0100 4139321 http://www.medworm.com/index.php?rid=4134093&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fz2phJf7UH7U%2F TweetOn BioStar the question is posed; How important is the long-term sustainability of data resources?. The question should be framed differently. Posed as such, it’s difficult to say anything other than “important”, but the reason we are in this state of URL decay and abandoned resources is culture. Resources are a means to get published, without any thought about whether wheels are being reinvented, long term sustainability and understanding (in many cases) of who the target audience is, how the resource might get used, or anything of that sort. I am a product guy and even in academia, we must treat resources as products, cause they are used by other researchers, even if those are a small number of collaborators. You need to think about why you are developing a particu... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4134093 Thu, 04 Nov 2010 02:25:59 +0100 4134093 http://www.medworm.com/index.php?rid=4125194&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FBZ3u3pzILmk%2F TweetA quick thought that occurred to me earlier this evening.  Will there ever be a time when programmers and informatics types in the sciences will find it more rewarding to take part in a data hacking effort on Kaggle? Perhaps I should rephrase that to, will others in the community value efforts in improving search algorithms using a Kaggle or community driven approach over a publication driven approach? Code is viewed as a way to get published, not as a way to get science done better. Yes, I am generalizing, but you get the point. And Github and others are waiting to be tapped, as is a philosophy of re-use, tapping APIs that others have written, etc. The funders in the sciences would be well to recognize the value of resources that can be leveraged by a global community, rather than s... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4125194 Mon, 01 Nov 2010 06:41:59 +0100 4125194 http://www.medworm.com/index.php?rid=4119746&cid=t_92073_155_f&fid=38407&url=http%3A%2F%2Fpathologyinformaticstrenches.blogspot.com%2F2010%2F10%2Foh-irony.html Let's talk about pathology informatics…the ironic side of pathology informatics, that is. Let's start this discussion by providing some background. So much of what a pathology informatician does is very serious. One false step and you could be on your way to mishandling the data for tens to hundreds to thousands of patients at one time. The stress alone can make some of us very cranky. OK, really cranky. Despite the fact that what we do is very important, it is often under-appreciated and usually under-recognized because it is in the background of many health care operations. That is, of course, until something goes wrong… However, outside of work, describing what I do for a living to my friends and family, many of whom are not in the medical or information technology (IT) profession... Pathology Informatics from the Trenches blogs http://www.medworm.com/rss/comments.php?id=4119746 Thu, 28 Oct 2010 21:41:00 +0100 4119746 http://www.medworm.com/index.php?rid=4119476&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FPvDVvw4jMlA%2F TweetI’ve written about Swivel in the past, but I never really got around to using it. Well Swivel is no more. Robert Kosara interviewed the co-founders about the rise and fall of Swivel (interestingly both had left Swivel prior to this news). Read the entire interview, but it reminded me about businesses and what might seem obvious with one thing doesn’t translate as well to others. But in the end it seems to be there were a lot of mistakes in execution. Perhaps Swivel was not the kind of business meant to be just it’s own business, but part of a larger operation. Perhaps they should have worked harder on the data sets they could get their hands on. I wasn’t there, so can’t say for sure and armchair backing is an easy exercise. I also think that a part of the... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4119476 Thu, 28 Oct 2010 06:10:01 +0100 4119476 http://www.medworm.com/index.php?rid=4098286&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FZzazp350H70%2F TweetThe Cytoscape FAQ has a very short developer FAQ, but it’s a good one. The question Why are there no biological semantics in the core, given that Cytoscape is targeted to biologists? The answer Biological semantics are poorly defined, so any model we build that assumes a given biological model will be wrong and will change frequently over time. By keeping the core of Cytoscape generic and free of bio semantics, we can add bio semantics as plugins as we need them and multiple people can add their own semantics without creating conflicts. Keeping biology out of the core helps us think a bit more generally about the functionality of the software. This is consistent with my recent talks on data platforms. It is important to innovate on the interfaces and not worry about the co... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4098286 Thu, 21 Oct 2010 02:39:12 +0100 4098286 http://www.medworm.com/index.php?rid=4086527&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F10%2Fmanaging-workflow-as-the-secret-sauce-in-diagnostic-information-systems.html Have you ever wondered why pathologists and radiologists would be unable to manage their daily work without their LISs, RISs, and/or PACSs whereas many clinicians balk at using hospital EMRs? One of the primary reasons for this difference is that these former systems manage professional workflow in the diagnostic services whereas clinical EMRs largely record the results of workflow decisions previously made by physicians and nurses. Because workflow support is not broadly integrated into the clinical EMRs, physicians understand that they may be able work more efficiently without them. This is one of the reasons why scribes are now being hired in some hospitals to enter data into clinical EMRs (see: Shift of Hospital EMR Data Entry Tasks from MDs to Scribes). Such an action, to the best of ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4086527 Wed, 20 Oct 2010 15:59:18 +0100 4086527 http://www.medworm.com/index.php?rid=4082158&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F10%2F18%2Finnovative-informatics-for-clinical-and-translational-researchers%2F On Friday, I attended this symposium sponsored by the National Center for Research Resources of the National Institutes of Health where the meeting was held. The symposium presented some of the latest software development for supporting research in academic medical centers. Topic areas included: Data Repositories for Research Participant Recruitment Tools and Strategies Clinical Information Systems and Research Study Management Systems Research Portal Innovations Some highlights include i2b2 as a data repository (Informatics for Integrating Biology and the Bedside) REDCap for research study management (Research Electronic Data Capture) – used in over 160 centers Vivo – enabling scientific collaboration – an impressive development using semantic technology. The scope o... eHealth blogs http://www.medworm.com/rss/comments.php?id=4082158 Tue, 19 Oct 2010 02:24:00 +0100 4082158 http://www.medworm.com/index.php?rid=4082262&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F9h-tJJ7jU0w%2F TweetAre the lines between designers, content creators / coders, and programmers blurring? Bob Boiko’s answer to that question is posted on the O’Reilly Radar. This part of his response caught my attention More specifically, in the center of a project you’ll find the information that the project collects, stores and delivers. Designers need to understand the structure of that information in order to present it. Content creators need to understand it to originate or edit it. Programmers need to understand it to build the machinery that moves it from place to place. In modern biology, we deal with information. We generate data and information, we consume information, we take actions based on that information. Yet, we do a terrible job of bringing designers, information gene... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4082262 Tue, 19 Oct 2010 02:15:13 +0100 4082262 http://www.medworm.com/index.php?rid=4061083&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F10%2Ffdiagnostic-delay-time-ddt-and-integrated-diagnostics.html One component of Diagnostic Adverse Events (see: New Attention Being Directed toward Diagnostic Adverse Events (DAEs)) is the Diagnostic Delay Time (DDT). I discussed the topic of diagnostic delays in a recent note, comparing them to Clinical Adverse Events (CAEs) (see: Breast cancer diagnostic delay depends more on race than insurance). Below is an excerpt from the DDT article as it relates to breast cancer: Race and ethnicity appeared to affect diagnostic delay more than insurance status for women with breast abnormalities, as revealed by data presented at [a recent conference].... Findings revealed that non-Hispanic black and Hispanic women with government or private insurance waited more than twice as long for a definitive diagnosis than non-Hispanic white women with government o... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=4061083 Tue, 12 Oct 2010 11:50:43 +0100 4061083 http://www.medworm.com/index.php?rid=4036651&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FI2KXB7sr2R8%2F Reviewing the latest applications for health professionals including iDoctor, CPR PRO app and the CPR PRO cradle (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4036651 Wed, 06 Oct 2010 06:42:53 +0100 4036651 http://www.medworm.com/index.php?rid=4031424&cid=t_92073_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=4027301&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F0h0O6JlWvO4%2F TweetI’ve written about various Jeff Bezos concepts on this blog before, and a recent, great, blog post by Bradford Cross highlighting Jeff’s Regret Minimization Framework got me thinking. Most of the discussions around long term thinking tend to be from the business standpoint, and I could write a long post just about how the biopharma industry should approach the business and science of drug development, but I think there’s a lot to apply to research science as well. Both from the researcher perspective and the funding agency perspective, I fear that our thinking is very short term. Despite the fact that the rewards from the science we do might be years out, our funding, whether it is for infrastructure or science projects tends to have the wrong priorities in mind. Lon... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4027301 Sun, 03 Oct 2010 21:07:47 +0100 4027301 http://www.medworm.com/index.php?rid=4025735&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FAWCxEW662Yk%2F TweetTo answer the right questions you need the right people That’s the last line from a blog post by Steve O’Grady. In Even with Big Data, it’s difficult to hard to ask the right question, Steve points out that with large amounts of data, asking the right question is quite hard. His point, channeling Kevin Weil, is that with a lot of data, asking the right questions becomes critical. In the sciences this gets magnified, because the questions we ask are critical to developing new hypotheses and as a former colleague of mine always said, it’s always about our point of view. In other words, framing questions is critical and the results we get depend on the questions we ask and how we are asking them. As we generate more and more biological data, our biggest challenge ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=4025735 Sat, 02 Oct 2010 07:55:24 +0100 4025735 http://www.medworm.com/index.php?rid=4003261&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FUzrv0EUWPa4%2F Software engineers working for UCEM at the Symantec Health Institute of Technology have confirmed slugtrails of the Stuxnet worm on several of the UCEM servers. Whilst initial reports suggest that US and Mossad agents might be using the worm to infiltrate the Siemens SCADA Management System of the Bushehr Nuclear Reactor in Iran, Professor Inglebert Struvite Staghorn of UCEM is concerned that a far more sinister motive, aimed at disrupting operations at Emergency Department Waiting Rooms is more likely. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4003261 Mon, 27 Sep 2010 15:56:54 +0100 4003261 http://www.medworm.com/index.php?rid=3999182&cid=t_92073_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=3993921&cid=t_92073_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FqvdyIPG4b-I%2F The one shot answer to electrical restraint and DC cardioversion. Drop the patient rendering them harmless in less than 0.47 seconds with the Police Grade, twin aeroflex gold tipped electrode 'stingers', with a range of up to 200 feet. Then defibrillate the victim out of excited delirium with a synchronized life saving biphasic 50,000 volt shock, and gift them the current of life. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=3993921 Wed, 22 Sep 2010 00:10:10 +0100 3993921 http://www.medworm.com/index.php?rid=3982087&cid=t_92073_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=3943035&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F09%2Fthis-is-a-guest-blog-note-by-dr-alexis-carter-director-of-pathology-informatics-at-emory-university-school-of-medicineat-e.html This is a guest blog note by Dr. Alexis Carter, Director of Pathology Informatics at Emory University School of Medicine. She discusses some of the pitfalls of the AP-LIS documentation of the names of pathologists who serve as consultants on a surgical pathology case.At Emory, we are currently in the process of upgrading our old AP-LIS to CoPathPlus.  During this upgrade, a number of issues have arisen that need to be resolved. Sometimes a new system can address new tasks, replacing previous manual/paper solutions. Sometimes the old system was able to perform tasks that the new system cannot. Sometimes neither system can deliver an acceptable solution.  One of the problems that we are struggling with falls into this last category. Pathologists frequently show surgical pathology... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3943035 Tue, 07 Sep 2010 13:39:37 +0100 3943035 http://www.medworm.com/index.php?rid=3933271&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F09%2Fi-recently-got-a-copy-of-the-book-that-kaiser-just-published-about-their-multi-billion-dollar-epic-deploymentconnected-for.html I received an email narrative from Dr. Bob Miller who is the Director of Pathology Informatics at Johns Hopkins. It was full of very useful information so I am posting it below as received. I am sitting on some other emails from him in a similar vein that I will also post in upcoming days. (BAF)I recently got a copy of the book that Kaiser just published about their multi-billion dollar Epic deployment: [Connected for Health: Using Electronic Health Records to Transform Care Delivery]. Unlike many similar tomes, which typically contain theories and grandiose plans, Kaiser's book contains hard facts and descriptions of what they have actually accomplished.  I would encourage you to look at a copy. I had a fascinating time a couple of weeks ago attending the VA's "VeHU con... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3933271 Fri, 03 Sep 2010 13:34:43 +0100 3933271 http://www.medworm.com/index.php?rid=3929464&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F09%2Frising-rate-of-esophageal-cancer-in-the-uk-relationship-to-obesity.html I came across an interesting news items about the rising rate of esophageal cancer in the U.K. This initially surprised me because I assumed that smoking/drinking were declining in the U.K. These behaviors have a causal relationship to squamous cell carcinoma of the esophagus, but read on (see: Oesophageal Cancer Rates In Men Up 50 Per Cent In A Generation, UK), Below is an excerpt from the article:Oesophageal cancer rates in men [in the U.K.] have risen by 50 per cent over the last 25 years, according to new figures....In 1983 around 2,600 men were diagnosed with oesophageal cancer ...and according to the latest figures around 5,100 men were diagnosed with the disease. The most dramatic rise was among men in their 50s, as rates increased by 67 per cent over the same period. Rates in women... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3929464 Thu, 02 Sep 2010 12:34:12 +0100 3929464 http://www.medworm.com/index.php?rid=3891789&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FcYQTfrxgPmA%2F It’s ACS time in Boston, and there is a steady stream of tweets from the conference which you can track. Prior to the conference there were a couple of topics related to chemistry on the web which I’ve been meaning to write about. Better late than never I guess. The first one is Chemicalize, a public website for adding chemical resolution to web browsing, chemical names and chemical structure files. The service “allows you to browse the web and see structures for chemical names (text) identified in the web page. For each chemical structure image generated, you can link through to predicted data from the structure. The service is free and will be useful to anyone wishing to add chemical structures and data to their web browsing experience.” Chemicalize comes to us fr... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3891789 Sun, 22 Aug 2010 21:17:58 +0100 3891789 http://www.medworm.com/index.php?rid=3890566&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FOfmWflVjxLQ%2F I’ve talked about my jealousy of geospatial apps before. One of the things about the geo space that I really like is the number of mashups around, enabled by companies like SimpleGeo. Brady Forrest has a great post on O’Reilly Rradar highlighting some of the mashups enabled by the Polymaps, a collaboration between SimpleGeo and Stamen Design. The part that caught my attention was the part where all the various sources used to create some of those gorgeous maps are discussed. I think that’s the kind of effort that’s required in the genome browser world. To some extent genome browsers are a commodity, or at least should be. Having good libraries that allow people to build tools that embed genome browsers, etc would be a great benefit to the community. Given that genom... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3890566 Sun, 22 Aug 2010 04:16:46 +0100 3890566 http://www.medworm.com/index.php?rid=3854761&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FjDCw12Nzuqk%2F With the ACGME visit just around the corner, we’ve begun the typical frantic scramble to ensure a 100% dotted-i and crossed-t count here at AMC.  Part of that dance included... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3854761 Tue, 10 Aug 2010 12:44:23 +0100 3854761 http://www.medworm.com/index.php?rid=3845239&cid=t_92073_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=3831425&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F08%2F06%2Fibm-initiative-to-improve-healthcare-quality-and-costs%2F Recently IBM announced a major initiative to address significant data problems in healthcare. Acknowledging the fact that data is in structured and unstructured format and from various sources, the task of integrating these data points into a individual dashboard format can enable better medical decision making.  One tool to enable this kind of data integration is their text analytics tools LanguageWare™ (LW) and Cognos Content Analyzer (CCA). Both of these were acquisitions by IBM in the past few years and it appears that they are now integrated enough to be used with large data sets in health care.  Analyzing unstructured information can benefit insurance companies as well. The tool looks like it combines natural language search and semantic technologies. The video illustrations the... eHealth blogs http://www.medworm.com/rss/comments.php?id=3831425 Sat, 07 Aug 2010 03:27:24 +0100 3831425 http://www.medworm.com/index.php?rid=3822871&cid=t_92073_87_f&fid=34765&url=http%3A%2F%2Fhcrenewal.blogspot.com%2F2010%2F08%2Ffew-comments-on-ge-radiation-debacle.html Due to my being busy with my HIT-related injured mother, Roy Poses beat me to posting about the General Electric CT over-irradiation debacle (GE: Don't Know Much About Radiation Safety, Don't Know Much About Physics).I am going to add two points:Point 1:The National Research Council in its 2009 report on health IT warned that "current approaches to healthcare IT are insufficient", and one of the major caveats was that:... greater emphasis should be placed on information technology that provides health care workers and patients with cognitive support, such as assistance in decision-making and problem-solving.In fact the lack of cognitive support for clinicians was one of the report's major themes."Cognitive support" by definition means producing devices (whether physical or virtual) that ar... Health Care Renewal blogs http://www.medworm.com/rss/comments.php?id=3822871 Wed, 04 Aug 2010 17:39:00 +0100 3822871 http://www.medworm.com/index.php?rid=3854763&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FJQTFx3BebIM%2F [Via C|Net Health Tech] C|Net’s Elizabeth Moore relays the recently released results of the 2010 Spyglass Consorting Group’s report entitled ‘Trends in Mobile... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3854763 Wed, 28 Jul 2010 03:20:55 +0100 3854763 http://www.medworm.com/index.php?rid=3787088&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FWYnan9rhGbA%2F Image via Wikipedia I am reading up a lot of Jim Gray these days, so a lot of his ideas are quite fresh in my head. Also had an interesting discussion with Nancy Parmalee on Twitter about software, informatics, bench scientists and small labs. One thing that jumped out, and is hardly a surprise, is that for the most part, there is a huge disconnect between the data science, and the scientists who need to make use of the work done by data scientists (often bench scientists). I’ve long argued that we neglect “infrastructure” software like data management systems, tracking systems, query systems, etc which all require well designed, scalable backends and should be treated like products, cause they are, even if they are home grown, or derived from open source software. Thi... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3787088 Mon, 26 Jul 2010 06:02:10 +0100 3787088 http://www.medworm.com/index.php?rid=3854766&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2Fj8A1Qvp7uAE%2F Here in the Albany Med Pathology Department we maintain what’s called ‘The White Box’.  This box (which is actually gray, IRL) is for interesting cases that pop up during sign-out... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3854766 Fri, 23 Jul 2010 14:46:05 +0100 3854766 http://www.medworm.com/index.php?rid=3784511&cid=t_92073_155_f&fid=39055&url=http%3A%2F%2Fjulesberman.blogspot.com%2F2010%2F07%2Fnew-book-coming-in-september.html If you've noticed a decline in my blogging of late, it's because I've been putting the finishing touches on my new book, Methods in Medical Informatics: Fundamentals of Healthcare Programming in Perl, Python, and Ruby, which will be published in September in the CRC Press series in Mathematical and Computational Biology.This book is a departure from my earlier language-specific works. The new book stresses descriptions of medical informatics algorithms, all presented in the following format:1) Each method has a background discussion, explaining how the method is used by healthcare professionals. 2) This is followed by a narrative description of each of the steps of the algorithm.3) Equivalent implementations of the algorithm are provided in Perl, Python and Ruby. Scripts draw data from fre... Specified Life blogs http://www.medworm.com/rss/comments.php?id=3784511 Fri, 23 Jul 2010 12:51:00 +0100 3784511 http://www.medworm.com/index.php?rid=3780431&cid=t_92073_113_f&fid=34631&url=http%3A%2F%2Fehealth.johnwsharp.com%2F2010%2F07%2F22%2Famerican-association-of-medical-colleges-group-on-information-resources%2F Next week I am attending a leadership institute of the AAMC in La Jolla, California. This week-long institute is by nomination – a group of 33 of us will attend, many CIOs and other leaders in healthcare IT and library science at academic medical centers. The program is very participatory with small groups making up much of the time as well as some lectures from a diverse faculty. Doing preparation for the institute has provoked thinking about leadership concepts and how to influence change in academic organizations. Although the term innovation is not explicit in the program, it certainly is on my mind as I prepare. One of the readings in preparation is from the book, Medicine and Business: Bridging the Gap by Sheldon Rovin, particularly chapter 3 on Leading Change. Also recommended... eHealth blogs http://www.medworm.com/rss/comments.php?id=3780431 Fri, 23 Jul 2010 01:43:57 +0100 3780431 http://www.medworm.com/index.php?rid=3854768&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FeqbRQdOyrxk%2F To be a pathologist is to be a teacher.   Whether it be giving resident lectures, conference presentations, tumor boards or even something as simple as in-house consults, we pathologists are... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3854768 Wed, 21 Jul 2010 16:00:09 +0100 3854768 http://www.medworm.com/index.php?rid=3746907&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2Fjesvqq0466A%2F In keeping with my recent data science theme, Ben Lorica has a nice post up on how to nurture data scientists. While his post focusses on data scientists in commercial organizations, the post has some very relevant points for bioinformaticians. After working in companies both large and small, it’s clear to me that the strict separation of tasks is the major obstacle faced by data scientists. The most common manifestation is the separation between data analysis and data management. In many large companies, most analysts/statisticians have to wait for data from a designated data warehousing team, and in a lot of cases they wait for data from multiple owners of different data warehouses. Neil pointed to another bit To nurture data scientists, companies need to focus more on culture and ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3746907 Tue, 13 Jul 2010 07:01:54 +0100 3746907 http://www.medworm.com/index.php?rid=3746793&cid=t_92073_107_f&fid=35026&url=http%3A%2F%2Fwicherts.socsci.uva.nl%2Fdatasharing.pdf This is a continuation of notes on iEVOBIO meeting.  Much of this comes from twitter.  Additional comments will be posted over the next few days.  See notes on Day 1 here. Note - thanks to the people who answered my query on twitter about how to remove spurious html code from pages - I wrote this post a few days ago but somehow the copying and pasting I did from twitter broke blogger with some weird html.  I ended up using Zubrag which was suggested by brendanwlocke. Day 2. Beginning. Since I was leaving that PM I could not borrow a hotel bike and bike over again.  So I walked from the hotel, along the river 2 or so miles, after getting coffee.  I got to the meeting a bit late and thus missed much of the opening Keynote, which was a bummer since it seem... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3746793 Tue, 06 Jul 2010 00:15:44 +0100 3746793 http://www.medworm.com/index.php?rid=3726624&cid=t_92073_107_f&fid=35026&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FTheTreeOfLife%2F%7E3%2F5SIfMzxO6C0%2Fsummary-of-ievobio-day-1-evolution.html Well, just getting around to writing up some thoughts on the iEVOBIO meeting I went to earlier this week.  It was really quite excellent so here are some thoughts/notes.  Today I am writing about the background and Day 1.  Most of this is simply a catalog of what happened along with some twitter details ... In a few days I will write up a post on what I think it meant .... The background: how I heard about iEVOBIO (skip to below if you just want to know about what happened in the meeting)   The first I heard about regarding the meeting was Dec 7, 2009, in a Direct Message on Twitter from @rdmpage.  That would be Rod Page, who I had never met, but followed remotely via twitter, his blog, his software and his papers.  He wrote Hi Jonathan, hope you got my ema... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=3726624 Mon, 05 Jul 2010 17:48:15 +0100 3726624 http://www.medworm.com/index.php?rid=3714366&cid=t_92073_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=3695825&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F06%2Freasons-why-dvm-pathologists-are-adopting-digital-pathology-faster-than-md-pathologists.html This is the second portion of guest blog note written by Steve Potts, PhD. The first was posted yesterday (see: Veterinary Pathologists Adopting Digital Pathology Faster than MDs). Steve is the CEO of Flagship Biosciences, a pathologist-owned CRO and provider of digital pathology services in the pharmaceutical and medical device industries.I would propose the following reasons why the adoption of digital pathology among DVM pathologists is faster than among their MD counterparts: Veterinary pathologists have benefited from the development of a strategic, forward-looking vision by pathologists working in executive management at the various pharmaceutical companies. These individuals are required to manage studies generating hundreds, if not thousands, of slides each and requiring review... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3695825 Thu, 24 Jun 2010 12:38:02 +0100 3695825 http://www.medworm.com/index.php?rid=3687300&cid=t_92073_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=3679876&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FNQwXPk4Pbp0%2F Admittedly, this post is as much of a test of my new WordPress 3 install, but it’s a cool one anyway. I’ve talked about curation with Freebase Gridworks before. In a recent blog post, Daniel Tunkelang points to Gridworks as well as one I wasn’t aware of, Needlebase. The Needlebase site has this really cool video showing how they build a quick database of travel info. The reason I point to these tools is that curating semi-structured data is something we have to do a lot in biology and chemistry. In the Needle case, there is some level of screenscraping involved as well or so it seems. The point is that we have a lot of curation to do in our space. I’d like to see people develop tools that can be made available, either as free or open source utilities or commercial o... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3679876 Mon, 21 Jun 2010 06:07:48 +0100 3679876 http://www.medworm.com/index.php?rid=3659168&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F06%2Fthe-criticality-of-performing-both-tc-and-pc-in-incources-labs.html Discussion: Insourcing of Pathology Specimens by Specialty Groups; Consideration of the Underlying Forces that Promote Pathology Insourcing). Pathology services, for reimbursement purposes, are separated into two components referred to as TC (technical component) and PC (professional component). The term global billing applies if a single fee is used to cover both parts. Joe Plandowski has shared with me a letter that he sent to Mark H. Stoler, M.D., president of the American Society for Clinical Pathology (ASCP), on March 31, 2010. In it he discusses the integration of insourced pathology services as they relate to TC and PC. I quote it below:Besides eliminating CMS payments to pod labs, I advocate eliminating CMS payments to any in-office anatomic pathology laboratory that is not perform... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3659168 Mon, 14 Jun 2010 12:04:37 +0100 3659168 http://www.medworm.com/index.php?rid=3648719&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FQFIusbj7hy8%2F Greg Linden points us to a clever paper (pdf) that makes great use of metadata associated with Flickr photos. Using semantic (tags) and geospatial (lat-long) information the authors are able to reference them again points of interest and reconstruct automatically intra-city travel itineraries. They then reference these against itineraries from professional sources (making great use of Amazon Mechanical Turk. Disclaimer: I work for Amazon Web Services). I still think we make relatively poor use of scientific metadata, e.g. I’d like to see instrument and condition related information made available as metadata with various experiments, as well as experimental conditions (at least the important bits), computational setup, etc. While admittedly there is less structure here, using simple ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3648719 Thu, 10 Jun 2010 04:13:54 +0100 3648719 http://www.medworm.com/index.php?rid=3648720&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FazZ8Ple_Ew4%2F Iddo Friedberg writes about a computational bridge to experiments … we need a good collaboration between those who do the computational work, and those who do the experimental work in identifying which are the most important books to look at, and what words in them we need to decipher first. The books that Iddo talks about are genomes and the words are genes. He is quite right. We might be living in a data-intensive world, and some might even argue for less data production, but I love the idea of targeted work and collaborations between computational and wet lab folks (I consider computation a form of experiment too). Most of my graduate work was a collaboration between me (computation), a molecular biologist and a biophysicist. One person developed the models (computation), then som... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3648720 Thu, 10 Jun 2010 03:23:52 +0100 3648720 http://www.medworm.com/index.php?rid=3645069&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F06%2Fw.html I recently posted a note announcing a webinar on the insourcing of pathology specimens (see: Webinar on the "Insourcing" of Pathology Specimens by Clinical Practice Groups). The title of the presentation indicates the need to "fight back" against the practice. Graham Grieve submitted the following comment: Why is [specimen insourcing] a threat to the specialty of pathology? Shortly afterward, Joe Plandowski sent the following note to me that I now offer to readers as a guest blog. What is wrong with "in-sourcing" of specimens by specialty groups? Consider these points: Many large, and not so large, GI and Uro specialists have moved out of the hospital into their own facilities for patient procedures (e.g., ASCs [ambulatory surgery centers] and Endoscopy Center... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3645069 Wed, 09 Jun 2010 12:06:33 +0100 3645069 http://www.medworm.com/index.php?rid=3621888&cid=t_92073_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=3618027&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F9s_RGXDI_10%2F Sean Saver writes about long term planning in the context of funding at P212121 (a great blog even if you are not a crystallographer). This reminds me of software development projects and long term planning in product development. In general, it’s good to have a long term goal and some sense of the macro steps required to get there, but you can’t be very specific beyond a few months (six tops in my mind). Things change, inputs change, and a plan is a constant re-adjustment of the inputs and trying to understand the impact. So in the context of funding, especially in fields related to fast moving technologies, where change is a given, perhaps we need the equivalent of “agile” funding. Perhaps submit a high level 2-5 year plan, but the actual specific goals and fundin... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3618027 Tue, 01 Jun 2010 06:33:29 +0100 3618027 http://www.medworm.com/index.php?rid=3595815&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F1qV5akSyZ9U%2F Sequencing vendors sell more instruments to individual labs than to big centers (or at least that’s what the word on the street is). I’ve always found that a little inefficient in the era of next-gen sequencing. Most labs will never be able to use instruments efficiently enough (the costs could drop to a level where that becomes a moot point, but that’s not the case right now). That’s why I like the idea of genome sequencing services. Dan Koboldt lists his reasons for the interest in services, but for me efficiency is the primary reason. I am also a fan of genomes being produced by high-throughput facilities and individual labs using that as a jump off point for biological discovery, mixing publicly available data (and there is a lot of that these days) with their s... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3595815 Tue, 25 May 2010 14:30:35 +0100 3595815 http://www.medworm.com/index.php?rid=3590452&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FcyKhRMzMcfc%2F The struggle between trying to please your committee and provide adequate support for the software you create remains. Is this a problem with the focus of graduate studies, the funding bodies, or the expectation of users? These words come from a post by Nils Homer up on Anthony Fejes’ blog. Nils talks about some of the challenges of being a software developer in the world of bioinformatics. In his post he quotes a friend … the software engineering and implementation of several of the methods consumed significantly more time and energy than the original research and paper writing. This is an important but less recognized component of methods development, as it prevents the work from remaining just interesting ideas, but puts them into practice For reasons Nils articulates so wel... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3590452 Sat, 22 May 2010 15:42:21 +0100 3590452 http://www.medworm.com/index.php?rid=3573866&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FB5SkvTRKfu0%2F One of the best posts ever on data management in the sciences comes to us via Titus Brown. The data management plan he proposes is one that is battle tested in many laboratories across the world. Neil captures the actionable items from the above blog post I am still laughing. I should be crying. Related articles by Zemanta Summer Course: Analyzing Next-Generation Sequencing Data (softwarecarpentry.wordpress.com) BEACON Funded! (softwarecarpentry.wordpress.com) (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3573866 Tue, 18 May 2010 04:18:58 +0100 3573866 http://www.medworm.com/index.php?rid=3564134&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FcDRwrV9yldU%2F I wonder if life science search engines study user patterns. Daniel Tunkelang has a great summary of Peter Morville’s talk at the Enterprise Search Summit. One of the core messages of the talk was that should we take the behavior patterns of information seekers and use them to inform design patterns for search user interfaces. One of the other ones was on faceted search. I actually think our search behavior is still evolving. When we go to a site like Pubmed, we search for an author, but where do we go from there? What kinds of facets are available? This gets even more interesting with richer interfaces like NextBio (which I still maintain is highly underrated). Both PubMed and NextBio could write papers on how people interact with search and search results. Here are some guesses on ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3564134 Fri, 14 May 2010 03:55:00 +0100 3564134 http://www.medworm.com/index.php?rid=3505071&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F-qLG_UxCPrY%2F I can’t quite put my finger on it, but something is amiss. On the other hand, something tells me that we are closer to an idea of a world with tools and components that can be assembled together by smart people in various ways. You could use something like GenePattern or Galaxy as a framework to embed these tools, or use Pipeline Pilot or Taverna. To build good science data platforms, we need to leverage abstractions. What is key is making sure that every layer of abstraction can successfully read and write from the one below and with other entities in the same layer. You have the algorithm developers, the platforms, the APIs and eventually the applications and analysis tools. You need a rich ecosystem of algorithm developers, data scientists (aka bioinformaticians) and software deve... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3505071 Mon, 26 Apr 2010 13:00:52 +0100 3505071 http://www.medworm.com/index.php?rid=3502928&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FjqaFjwIK1Z0%2F At the Sage Congress, one of my favorite talks was one that Atul Butte gave on using publicly-available data. I have long thought that actually performing microarray gene expression experiments would go away, since there will be sufficient compendia and public data available that can be used for doing all kinds of useful science. Atul’s talk drove that point home with some authority. His premise was that there is a lot of public data out there and while it may not always be perfect, smart people can use this data to do a lot of interest things, such as identifying data-driven candidate genes. In other words, use the data to find candidates and then drill down into the science. His other example was work by Joel Dudley (who happens to be sitting next to me as I type this), creating a ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3502928 Sat, 24 Apr 2010 19:19:39 +0100 3502928 http://www.medworm.com/index.php?rid=3499330&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2Fg_NIim0KH5s%2F   I guess it’s not that wild of an idea, but I love it.  Medgadget posted today about a California-area hospital that’s rolling 100 iPads out to their doctors so they can “keep... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3499330 Thu, 22 Apr 2010 20:48:56 +0100 3499330 http://www.medworm.com/index.php?rid=3494560&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F04%2Foptical-scanning-of-sputum-smears-for-tubercle-bacilli-1.html The fastest growing technology in the field of pathology and lab medicine is digital imaging and, tangentially, the use of algorithms in the interpretation of digital images. This latter technology is commonly used in connection with IHC and FISH-stained slides to quantify a previously subjective interpretation. Now it turns out that image analysis and algorithms may also be of value in the identification of tubercle bacilli in microbiology labs in developing countries (see: Technology: For Nations That Lack the Expertise, an Automated System for Detecting TB):One of the difficulties of diagnosing tuberculosis is that there is no simple blood or urine test. Instead, a laboratory technician must take a sample of sputum coughed up from the lungs, stain it and inspect it under a microscope f... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3494560 Thu, 22 Apr 2010 12:00:00 +0100 3494560 http://www.medworm.com/index.php?rid=3487389&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FC6jBQcBT1y8%2F As a result of the move and the associated (and dreaded) cleaning out of our offices, I have since become the beneficiary of quite a few forgotten “treasures” from around the department.... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3487389 Mon, 19 Apr 2010 19:30:57 +0100 3487389 http://www.medworm.com/index.php?rid=3472062&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2F-QMi0Jwi1XY%2F Our department here at Albany Medical Center has been searching for a cover-slipping solution for some time now.  Their searching brought them to the Ventana Symphony H&E Discreet Slide Stainer.... Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3472062 Wed, 14 Apr 2010 16:49:09 +0100 3472062 http://www.medworm.com/index.php?rid=3467953&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2F3DvNX9dRz3w%2F Maria Hodges has a fantastic post about building (bad) biological databases, a must read. The only point I might have a little nit about is Tip #5, Totally trust your automated systems. Little because biological data does often need some curation due to the nature of the beast, but I would argue that some of the largest data systems in the world are completely, or near completely automated, so it’s possible. (Source: business|bytes|genes|molecules) business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3467953 Wed, 14 Apr 2010 02:43:08 +0100 3467953 http://www.medworm.com/index.php?rid=3463869&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F04%2Fbinge-drinking-in-wales-trends-in-alcohol-consumption.html The Wall Street Journal recently ran a fascinating article on the increase in binge drinking with special attention to Cardiff, Wales (see: U.K. Drinking Problem Gets Political; subscription required). One of the take-home lesson in it was that much of the excessive drinking by the youth in the U.K. was related to cheap alcoholic beverages offered in supermarkets, causing the pubs compete by lowering their prices. Contained in the article was a fascinating chart tracking alcohol consumption in OECD countries. I present it here for your review.   Spend a little time examining these data. Here are just a few of my own observations and questions: Note the decline in alcohol consumption in Turkey as the country has moved from a secular political orientation to broader adoption of Islam. ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3463869 Tue, 13 Apr 2010 12:14:39 +0100 3463869 http://www.medworm.com/index.php?rid=3456830&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FEYegF9m_eeA%2F I recently blogged about reference implementations, talking about work by Pete Skomoroch (one of those folks like Pierre and Rajarshi whose ability to churn out cool programming/data analysis stuff makes me feel completely insignificant). Pete commented on that post, asking the following question, which I include here. I’d love to get a broader discussion of the general question. I think this is the kind of thing that prompted the idea of The Biogang and what Github was meant for Can you think of a tightly framed problem in bioinformatics, like predicting movie ratings for the the Netflix Prize? If people are looking to do one of these examples, I’d suggest that building an open source app that manages contest submission and evaluation like Netflix, but for bioinformatics. Bas... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3456830 Sat, 10 Apr 2010 04:51:52 +0100 3456830 http://www.medworm.com/index.php?rid=3433093&cid=t_92073_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=3412549&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FJ23P0DOEMpI%2F Image via CrunchBase I found out about Freebase Gridworks through a post by Jon Udell. In the post, Jon refers to two screencasts on this yet unreleased product. In the Freebase blog post, they quote the announcement from the mailing list. The important bits We at Metaweb strongly believe that Freebase can be helpful not only as a giant repository of heavily curated and interconnected data but also as a way to help people cleanup and integrate their own datasets by aligning their data with a shared substrate. Jon adds to this after seeing the screencasts As the open data juggernaut picks up steam, a lot of folks are going to discover what some of us have known all along. Much of the data that’s lying around is a mess. That’s partly because nobody has ever really looked at it. As a n... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3412549 Sun, 28 Mar 2010 14:00:25 +0100 3412549 http://www.medworm.com/index.php?rid=3412550&cid=t_92073_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=3387000&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FbkcTTVT2m5U%2F Image via Wikipedia In my day job, I get to see a lot of innovative geo-related software and services, and the O’Reilly Radar does a great job of tracking innovations in this space. SimpleGeo, WeoGeo, ESRI, Loki, Cloudmade, Quantum GIS, GeoCommons, etc are just some examples of companies/organizations/open source projects doing very interesting things around geospatial data of all kinds. There are a number of good open source efforts around geo-data and visualization, and I am almost certain I am missing a ton. These toolkits allow people to do interesting things. So where am I going with this? Somehow there seems to be a lack of similar interesting things with scientific data. Admittedly that is a gross generalization, but outside of things like Rich Apodaca’s many project... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3387000 Sun, 21 Mar 2010 06:50:25 +0100 3387000 http://www.medworm.com/index.php?rid=3374401&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F03%2Ftax-on-soda-pop-for-better-health-gains-momentum.html Excise taxes on unhealthy foods or substances like tobacco have an irresistible appeal to state and national politicians. They help to correct budget deficits, particularly in hard economic times. They can also be said to improve consumers' health status. For many, however, they represent an unwarranted intrusion of public policy into our lives. Others reply, in response, that the benefits of such taxes outweigh the harm. I have written previously about this same topic (see: Federal Tax on Soda Pop Proposed: Can This Be Justified?). Below is an excerpt from a recent article that summarized recent activity in this area (see: Health officials ready to make push for statewide soda tax):Health officials are ready to make the final push for a statewide tax on sugary drinks [in the state of ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3374401 Wed, 17 Mar 2010 12:41:51 +0100 3374401 http://www.medworm.com/index.php?rid=3354595&cid=t_92073_155_f&fid=38406&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FThe1xObjective%2F%7E3%2FH96PxRIxWFs%2F Follow me on Twitter: https://twitter.com/1xObjective Catch the rest of the story after the break... (Source: The 1x Objective) The 1x Objective blogs http://www.medworm.com/rss/comments.php?id=3354595 Thu, 11 Mar 2010 16:04:24 +0100 3354595 http://www.medworm.com/index.php?rid=3342921&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F03%2Fcorrelation-of-socioeconomic-status-and-engagement-in-cancer-screening-programs.html Of great interest to me is the strong correlation of good health and long life with one's level of education. It's a much stronger correlation than even wealth and socio-economic status. On the face of it and in order to explain this finding, one might surmise that more educated people have a better understanding about how to preserve their health or seek therapy when sick. There is also an interesting parallel theory that educated people have invested time and money over many years in themselves, postponing their high-earning years to later in life. A conclusion, based on this scenario, is that their concern for better health results from a desire to extend their careers and earning power later in life. A recent article about sociodemographic status and cancer screening provides a... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3342921 Mon, 08 Mar 2010 12:31:48 +0100 3342921 http://www.medworm.com/index.php?rid=3338388&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FnXks1nQdnsQ%2F Image via CrunchBase I’ve always been intrigued by the concept of a reddit or Digg style system for scientific queries. When StackOverflow came along, it was clear (to me at least) that a StackOverflow-like system was the future of technical Q*A sites. Enter StackExchange, which provides exactly that, and StackExchange sites have been sprouting up around the web. Egon started one for Blue Obelisk, and Rich Apodaca started one on experimental chemistry. The latest entrant is one I’ve already spent some time on, BioStar. The site was started, or so it seems, by Istvan Albert (the bot resolves to his email address) and is focussed on bioinformatics and computational biology. It’s still a small site and in bootstrap mode. Hopefully it will get a good audience and progress ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3338388 Sat, 06 Mar 2010 04:25:52 +0100 3338388 http://www.medworm.com/index.php?rid=3298624&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F02%2Fobesity-as-a-cause-of-death-on-death-certificates.html This article touches on a number of key points in the relationship of obesity to autopsy findings and the cause of death as recorded by clinicians on death certificates. The following questions come to my mind as I consider this general topic: (1) should obesity be viewed as a disease or medical condition; (2) at the time of death, should morbid obesity be considered as a primary or a contributing cause of death; (3) what criteria should be used to determine whether obesity is a primary or contributing cause of death. In order to explore these questions in greater depth, I Googled the terms obesity and cause of death. I first discovered a 2004 article quoting the CDC and indicating that obesity was a common underlying and preventable cause of death (see: Obesity approaching tobacco as top ... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3298624 Tue, 23 Feb 2010 12:47:06 +0100 3298624 http://www.medworm.com/index.php?rid=3287842&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fgreen-cda%2F Less fat or half baked? (Source: symtym) symtym blogs http://www.medworm.com/rss/comments.php?id=3287842 Fri, 19 Feb 2010 08:24:17 +0100 3287842 http://www.medworm.com/index.php?rid=3283839&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F02%2Fthe-toyota-way-lean-and-six-sigma.html My previous blog notes have been somewhat critical of one aspect of the Lean and Six Sigma approach to lab management. I have no problem with these management techniques as long as they are viewed as only one facet of a total lab management program and do not crowd out other approaches such as strategic planning. Here's a quote from a note I posted last October (see: Some Laboratory Managers Getting Carried Away by Lean/Six Sigma Projects):...[L]ab personnel who spend most of their time worrying about "how" or "comment" questions may be too involved with improving daily work processes and perhaps avoiding some of the more challenging "why" or "pourquoi" questions....In order to begin to explore some of these strategic "why" questions, i... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3283839 Thu, 18 Feb 2010 13:00:00 +0100 3283839 http://www.medworm.com/index.php?rid=3272986&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fmeaningful-x%2F Should Doctors Reject the Government’s EHR Incentive Plan?—David Kibbe It’s a big hill to climb for a carrot that may not be there when you reach the top. Is health information technology (IT) being set up to fail? Might we be facing a lost generation of health IT investment? Will Kaiser Permanente and Mayo Clinic get windfall profits while small practices receive nothing but hassles? It’s beginning to seem that way. Valid questions in this excellent article by Kibbe. A physician must consider many factors in coming to a decision on whether and when to participate in the HITECH incentives program. HITECH Physician Incentives (carrots and sticks)   Adopt2011 Adopt2012 Adopt2013 Adopt2014 Fail toAdopt 2011 $18K         2012 $12K $18K &n... symtym blogs http://www.medworm.com/rss/comments.php?id=3272986 Mon, 15 Feb 2010 08:45:00 +0100 3272986 http://www.medworm.com/index.php?rid=3269760&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fhealth-information-startup-funding%2F Sebelius, Solis Announce Nearly $1 Billion Recovery Act Investment in Advancing Use of Health IT, Training Workers for Health Jobs of the Future Health and Human Services Secretary Kathleen Sebelius and Labor Secretary Hilda Solis today announced a total of nearly $1 billion in Recovery Act (ARRA) awards to help health care providers advance the adoption and meaningful use of health information technology (IT) and train workers for the health care jobs of the future. The awards will help make health IT available to over 100,000 hospitals and primary care physicians by 2014 and train thousands of people for careers in health care and information technology. This Recovery Act investment will help grow the emerging health IT industry which is expected to support tens of thousands of jobs ran... symtym blogs http://www.medworm.com/rss/comments.php?id=3269760 Sat, 13 Feb 2010 09:30:11 +0100 3269760 http://www.medworm.com/index.php?rid=3259294&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F02%2Fththe-use-of-irony-in-appealing-to-young-male-adults-for-std-testing.html It can be a challenge to reach young adults with public health messages, particularly adult males (see: The Mind of the Young Adult Male and On-Line Health Education; More on Reaching Young Males with Public Health Education Messages). Hold that thought while I briefly discuss web-based direct access testing (DAT). These are web sites that enable the ordering of lab tests at a reasonable price, paid for with a credit card, and without the intermediation of a physician. Some state laws prohibit this practice. A niche market of direct access testing are those web sites that offer only lab tests to diagnose sexually transmitted diseases (STDs).I blogged about this topic in November three years ago (see: Direct Access Testing for STDs). Michelle Sobel of Analyte Media is an expert at cra... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3259294 Wed, 10 Feb 2010 13:14:34 +0100 3259294 http://www.medworm.com/index.php?rid=3251283&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fmeaningful-barrier%2F Companion posts: Meaningful Absence, Meaningful Use: rules, not people! When behaviors (broadly construed) are incentivized, and exchanges amongst behavioral–states likewise incentivized, are we not summing the behavioral constraints of all? Will meaningful absence lead to a meaningful barrier? The three goals of meaningful use: Incentivize certified EHRs. Incentivize exchanges amongst certified EHRs. Self–validate a certified EHR with the production of meaninful use measurements. Meaningful Use (1x): incentivized behavior Meaninful Use (zoom out 10x): incentivized exchanges Meaningful Barrier (zoom out 100x) (Source: symtym) symtym blogs http://www.medworm.com/rss/comments.php?id=3251283 Sun, 07 Feb 2010 21:24:56 +0100 3251283 http://www.medworm.com/index.php?rid=3248607&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fmeaningful-use-rules-not-people%2F Hattip to Heather on the title. Adapted from Federal Register January 13, 2010: Medicare and Medicaid Programs: Electronic Health Record Incentive Program , 1844–2011 [E9–31217] (TXT)(PDF) Meaningful Use (Stage 1, 2011): Responsible Entities, Patient Recipient Eligible Professional (EP) Eligible Hospital (EH) Unique Patient (UP) CPOE for 80% of all orders CPOE for 10% of all orders   implement Drug-Drug, Drug-Allergy, Drug-Formulary checks implement Drug-Drug, Drug-Allergy, Drug-Formulary checks   maintain an up-to-date Problem List of current and active diagnoses for 80% of UPs seen maintain an up-to-date Problem List of current and active diagnoses for 80% of UPs admitted   75% of all permissible prescriptions written by EP are transmitted electronically ... symtym blogs http://www.medworm.com/rss/comments.php?id=3248607 Sun, 07 Feb 2010 01:23:08 +0100 3248607 http://www.medworm.com/index.php?rid=3248663&cid=t_92073_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=3248608&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F02%2Fmeaningful-absence%2F What are incentives? Incentives are governmental monetary–inducements for entities to offer a product or provide a service. What is an EHR? An EHR is an electronic health record, funded in whole or in part by governmental incentives, subsequently certified, and capable of producing meaningful use. What is Certification? Certification is a process, conducted by a third–party entity (e.g., TJC), certifying that an EHR passes governmentally defined regulations and standards and capable of producing meaningul use. What is Meaningful Use? Meaningful use is the necessary work products of a certified EHR required to substantiate eligibility for governmental incentives. What is an Eligible Hospital? An eligible hospital is a hospital that is eligible to receive governmental inc... symtym blogs http://www.medworm.com/rss/comments.php?id=3248608 Sat, 06 Feb 2010 22:25:21 +0100 3248608 http://www.medworm.com/index.php?rid=3239589&cid=t_92073_105_f&fid=36987&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FIvorKovicMd%2F%7E3%2FYDZs7IjV63Q%2F Today, journalist Alain Ochoa (@alainochoa) conducted an interview on Twitter with me for Diario Médico (@diariomedico), Spain’s leading medium for health professionals. We mainly talked about mobile technology and its use in medicine. Follow the link to read the whole tweeterview titled Mobile health from Croatia. Tweet This Post (Source: Ivor Kovic, M.D.) Ivor Kovic, M.D. blogs http://www.medworm.com/rss/comments.php?id=3239589 Wed, 03 Feb 2010 18:19:19 +0100 3239589 http://www.medworm.com/index.php?rid=3236119&cid=t_92073_155_f&fid=36522&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fpathtalk%2F%7E3%2F1OumXo13uI8%2F1916 In December’s issue of the American Journal of Clinical Pathology there is an interesting editorial by Dr. Mark Wick that discusses Pathology 2.0 in reference to two articles in the journal. In summary, I think he feels there are uses in place for education and e-publications that are suitable and practical but thinks there are more serious considerations related to patient care, online communities related to diagnosis and/or treatment and patient privacy and security. A brief look at his website (see link above) I think emphasizes these points and makes use of educational and informational services without being directly interactive with a patient or another health care provider/pathologist. He concludes in his editorial: “Where, then, does this leave the status of Web 2.0 wi... pathtalk.org blogs http://www.medworm.com/rss/comments.php?id=3236119 Wed, 03 Feb 2010 02:04:33 +0100 3236119 http://www.medworm.com/index.php?rid=3224905&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fhealth-information-commons%2F The commons refers to resources that are collectively owned. There are two tragedies that may befall a commons: The Tragedy of the Commons and The Tragedy of the Anticommons. Paraphrasing Michael Heller (Gridlock Economy): the tragedy of the commons is when too many people share a single resource, we tend to overuse it; and the tragedy of the anticommons is when too many people own a single resource, and anyone can block the use. Modifying this for healthcare, the tragedy of the healthcare anticommons is that too many people own portions of a patient’s health information (HI), and anyone at anytime can block a full rendering of the patient’s HI. A patient’s HI might be charcterized by those that have an interest in the HI, including the patient. This interest extends beyo... symtym blogs http://www.medworm.com/rss/comments.php?id=3224905 Sun, 31 Jan 2010 06:43:32 +0100 3224905 http://www.medworm.com/index.php?rid=3223504&cid=t_92073_155_f&fid=39055&url=http%3A%2F%2Fjulesberman.blogspot.com%2F2010%2F01%2Fone-way-hash-perl-python-ruby.html I have prepared short scripts , in Perl, Python, and Ruby, for implementing one-way hash operations. One-way hashes are extremely important in medical informatics. The following text is extracted from a public domain document that I wrote, in 2002 (1).A one-way hash is an algorithm that transforms a string into another string is such a way that the original string cannot be calculated by operations on the hash value (hence the term "one-way" hash). Examples of public domain one-way hash algorithms are MD5 and SHA (Standard Hash Algorithm). These differ from encryption protocols that produce an output that can be decrypted by a second computation on the encrypted string.The resultant one-way hash values for text strings consist of near-random strings of characters, and the length of the str... Specified Life blogs http://www.medworm.com/rss/comments.php?id=3223504 Sat, 30 Jan 2010 12:32:00 +0100 3223504 http://www.medworm.com/index.php?rid=3223444&cid=t_92073_132_f&fid=35011&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmndoci%2F%7E3%2FKN_I2U5e3eI%2F Rich Apodaca has a great set of blog posts on using PubCouch, the CouchDB interface for PubChem. The series is great in itself, but I was especially intrigued by the title of the third installment, PubCouch: Streams Aren’t Just for Pipeline Pilot. In the post Rich describes how PubCouch makes it possible to work with the PubChem FTP archive like it was a single large SD file. Recently, I’ve started believing that modern programming paradigm and increasing awareness of RESTful architectures, distributed data processing, messaging etc makes systems like Pipeline Pilot look somewhat dated. They aren’t going to go anywhere soon, but I believe that the power of being able to deliver services to the end user is becoming the norm and developing those services is getting easier ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=3223444 Sat, 30 Jan 2010 03:56:30 +0100 3223444 http://www.medworm.com/index.php?rid=3212620&cid=t_92073_155_f&fid=34629&url=http%3A%2F%2Flabsoftnews.typepad.com%2Flab_soft_news%2F2010%2F01%2Fthe-mind-of-the-young-adult-male-and-online-health-education.html Previously discussed here has been the topic of on-line public health education and the use of smartphones as efficient channels to reach the young adult population (see: Placing Public Health Announcements on Google as Paid Ads, Seeking Solutions to the Chronic Disease Epidemic, Making e-Health Information Accessible with Smart Phones, The Mobile Web and the Future of eHealth). This approach is particularly relevant for messages relating to sexually transmitted diseases (STDs) such as Chlamydia. It is for this reason that I paid close attention to a recent article regarding the adult male television viewership, or rather the lack thereof, of Conan O"Brien (see: O’Brien Undone by His Media-Hopping Fans). For those of you who distance themselves from popular culture, O'Brien rece... Lab Soft News blogs http://www.medworm.com/rss/comments.php?id=3212620 Wed, 27 Jan 2010 12:39:08 +0100 3212620 http://www.medworm.com/index.php?rid=3208501&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fgrassleys-questions-on-hit%2F As Ranking Member of the Senate Committee on Finance, which has jurisdiction over the Medicare and Medicaid programs, I have a special responsibility to protect the health of the programs’ more than 100 million beneficiaries as well as the congressionally authorized tax dollars used to fund these programs. This includes ensuring the effective and efficient use of taxpayer money by the health care industry in implementing Health Information Technology (HIT), such as Computerized Physician Order Entry (CPOE) systems and Electronic Health Records (EHR). In recent legislation, approximately $19 billion in taxpayer funds was appropriated to encourage development and implementation of HIT systems, which further emphasizes the importance of responsible use and thorough oversight. Over the p... symtym blogs http://www.medworm.com/rss/comments.php?id=3208501 Tue, 26 Jan 2010 04:13:32 +0100 3208501 http://www.medworm.com/index.php?rid=3208502&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fgrassleys-concerns-on-hit%2F Grassley asks hospitals about experiences with federal health information technology program WASHINGTON—Senator Chuck Grassley has sent letters to 31 hospitals nationwide asking about their experiences in implementing the $19 billion federal health information technology program launched last year. “Given the taxpayer investment and the investment of the health care system overall in the information technology industry, the more Congress and others overseeing implementation of this program dig into the problems and work to get them sorted out now, the better,” Grassley said. “Hospitals are on the front lines and their perspective will be very valuable in this effort, so I look forward to hearing what they have to say about expanded use of health care information te... symtym blogs http://www.medworm.com/rss/comments.php?id=3208502 Tue, 26 Jan 2010 04:12:21 +0100 3208502 http://www.medworm.com/index.php?rid=3208504&cid=t_92073_114_f&fid=34963&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fdoctor-do-you-speak-flower%2F BTR: Doctor: Do You Speak “Flower”?, 1.26.10 0900 PST, hosted by @2healthguru What is flower? At this time it’s an abstraction—a placeholder for several concepts centering on what would healthcare look like if…? And, more specifically what would personal health information (PHI) look like if…? A flower was chosen as the abstraction because it is easily and universally understood, regardless of language, anywhere in the world—a flower is a flower. Where a flower is flower carries the additional abstraction that there is a common ground—characterized by property and implementation. While a fluid and dynamic idea, this informed panel will provide both history and context for its genesis and diverse unfolding narrative. Join Dirk Stanley, MD, @dir... symtym blogs http://www.medworm.com/rss/comments.php?id=3208504 Tue, 26 Jan 2010 03:11:52 +0100 3208504 http://www.medworm.com/index.php?rid=3163782&cid=t_92073_88_f&fid=38961&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fhypothetical-health-information-federation%2F Columbia is a fictional city of 1.5 million in the fictional state of Jefferson. The greater Columbia catchment area has a population of 3 million. There are four integrated healthcare systems in Columbia. The healthcare systems are associated with ten hospitals, dozens of clinics and skilled nursing facilities, over one hundred pharmacies, over one thousand physicians, and several hundred ancillary services. Columbia’s population utilize emergency services with an average incident rate of 0.35, consistent with the rest of the state and country. Thirty–five percent of the population goes to the ER every year, with 10% arriving by ambulance. The annual ER and EMS censuses are 1.05 million and 300,000 respectively. On any given day there are 2,877 ER visits and 822 ambulance tran... quanta vie blogs http://www.medworm.com/rss/comments.php?id=3163782 Tue, 12 Jan 2010 05:05:06 +0100 3163782 http://www.medworm.com/index.php?rid=3163783&cid=t_92073_88_f&fid=38961&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fhealth-information-communication-models%2F There appears to be two distinct (+overlap) models for health information communications. One uses the seven–layer OSI Model which seems dominate in the health informatics community (including HIT vendors, cats). The other uses the four–layer TCP/IP Model, the Internet Model, seen in the health internet community (dogs). The importance of the distinction is over whether or not content and transport are treated separately. No separation is more representative of the health informatics community. The health internet community handles them separately. Where there is no separation, there is the need to assert specialized standards for the transport of health information (e.g., HL7). Where there is separation, there is a belief that the security and privacy standards are sufficientl... quanta vie blogs http://www.medworm.com/rss/comments.php?id=3163783 Tue, 12 Jan 2010 01:03:35 +0100 3163783 http://www.medworm.com/index.php?rid=3159730&cid=t_92073_88_f&fid=38961&url=http%3A%2F%2Fsymtym.net%2F2010%2F01%2Fhealth-information-federation%2F A health information federation (HIF) might be defined as a health informational construct where there is no need for interoperability or health information exchange (HIE). To do so requires the health information content (data) to use structure–standard(s). Structured data, conforming to a structure–standard, is data that is machine readable (computable) in its native form. To eliminate the need for HIE requires that all participants within the HIF share a common structured data infrastructure. Interoperability becomes moot because such an infrastructure is, by design, wholly–operable. Interoperability and the use of HIE may be the most significant barriers (cost and technology) to widespread availability of health information. A HIF may be further characterized by a com... quanta vie blogs http://www.medworm.com/rss/comments.php?id=3159730 Mon, 11 Jan 2010 10:38:37 +0100 3159730