Future of Health IT: Trends and Scenarios

links for 2009-02-27

• Browser market share
  Browser statistics.
  (tags: seo browser+stats)
• Browser Statistics
  Name says it all.
  (tags: seo browser+stats)

links for 2009-02-18

• More People, Not Just More Stuff: Developing a New Vision for Research Cyberinfrastructure | EDUCAUSE CONNECT
  This ECAR research bulletin highlights a special academic program at the Syracuse University School of Information Studies that has been developed with the express purpose of creating a new information professional: the cyberinfrastructure facilitator (CI-facilitator).
  (tags: research society+and+culture information+technology IT+infrastructure)

links for 2009-02-17

• ISO 8601 Formats for Dates and Times
  'ISO 8601 is an international standard for the formatting of dates and times. It has been adopted by most of the major countries around the world, either directly or as equivalent national standards. Clock and hourglass. There are a number of options in the standard but the basic idea is that a date is normally represented in the Year-Month-Day format with the Year being four digits and the Month and Day both two digits. Similarly a time is shown as Hour:Minute:Second with each being two digit numbers. '
  (tags: iso iso+8601 date datetime time)
• International standard date and time notation
  'International Standard ISO 8601 specifies numeric representations of date and time. This standard notation helps to avoid confusion in international communication caused by the many different national notations and increases the portability of computer user interfaces. In addition, these formats have several important advantages for computer usage compared to other traditional date and time notations. The time notation described here is already the de-facto standard in almost all countries and the date notation is becoming increasingly popular.'
  (tags: programming reference software iso iso+8601 datetime time date documentation)
• Sources for Time Zone and Daylight Saving Time Data
  'The public-domain time zone database contains code and data that represent the history of local time for many representative locations around the globe. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight-saving rules. This database (often called tz or zoneinfo) is used by several implementations, including the GNU C Library used in GNU/Linux, FreeBSD, NetBSD, OpenBSD, Cygwin, DJGPP, AIX, Mac OS X, OpenVMS, Oracle Database, Solaris, Tru64, and UnixWare.'
  (tags: programming reference iso iso+8601 library software database)
• Seed: Seed Salon: Albert-Laszlo Barabasi + James Fowler
  'Barabasi: It is becoming a truism that we're living in the era of networks. Just about anywhere we turn, we encounter one. We have the World Wide Web and the internet; we have social networks, genetic networks, and biochemical networks. These things — web pages, genes, chemicals in our cells — are nothing new. What is new is that everybody's waking up to the fact that there is a network behind all of these systems, and we need to think about networks as a common feature of all complex systems. But I don't know if that's the way you see it.'
  (tags: social+networks network+analysis network+theory complexity)

links for 2009-02-16

• $900K NIH Research Grant Awarded to Study and Prevent Adverse Drug Reactions: UMD News: January 21, 2009
  'University of Minnesota Duluth professor Ted Pedersen and University Minnesota Twin Cities professor Serguei Pakhomov have been awarded a three-year, $935,000 National Institutes of Health research grant to develop natural-language processing (NLP) techniques that search through medical records to quickly detect widespread adverse drug reactions.'
  (tags: biomedical+informatics)
• Is technology producing a decline in critical thinking and analysis? / UCLA Newsroom
  'University of California, Los Angeles (UCLA) professor Patricia Greenfield says that critical thinking and analysis skills decline the more people use technology, while visual skills improve. Greenfield, the director of UCLA's Children's Digital Media Center, analyzed more than 50 studies on learning and technology. She found that reading for pleasure improves thinking skills and engages the imagination in ways that visual media cannot.'
  (tags: education hci psychology media learning information+technology)
• W3C: Interoperability Key to Social Networking
  'The World Wide Web Consortium, in a report on the future of social networking, cites the need for an interoperable distributed social Web framework. The W3C report concludes that applications should share profiles and data across networks so that social networking companies can grow and open further Web 2.0 possibilities.'
  (tags: social+networking w3c interoperability)
• Software speeds up molecular simulations
  '"Simulations that used to take three years can now be completed in a few days," said Vijay Pande, an associate professor of chemistry at Stanford and principal investigator of the Open Molecular Mechanics (OpenMM) project. "With this first release of OpenMM, we focused on small molecular systems simulated and saw speedups of 100 times faster than before." '
  (tags: biomedical+informatics bioinformatics visualization infoviz HCI)
• HPCwire: Berkeley Releases Cloud Computing Study
  'Cloud computing refers to both the applications delivered as services over the Internet and the hardware and systems software in the datacenters that provide those services. The services themselves have long been referred to as Software as a Service (SaaS). The datacenter hardware and software is what we will call a cloud. When a cloud is made available in a pay-as-you-go manner to the general public, we call it a "public cloud"; the service being sold is utility computing. We use the term "private cloud" to refer to internal datacenters of a business or other organization, not made available to the general public. Thus, cloud computing is the sum of SaaS and utility computing, but does not include private clouds.'
  (tags: cloud+computing information+technology)
• Agile world’s a stage - SD Times On The Web
  'Corporate trainer Matt Smith says that actors often must overcome their anxieties, a situation that parallels that of software developers. "If we're going to do Scrum and agile, we have to come to terms with that feeling and stop perceiving it as something to run from," he says. Certified Scrum trainer Stacia Broderick says the key to successful collaboration is a lack of inhibition, combined with frankness and a willingness to propose any concept.' - ACM TechNews
  (tags: software development physio-mimi)
• Sensors Help Keep the Elderly Safe, and at Home - NYTimes.com
  'Sensors and other monitoring technologies offer senior citizens more freedom to live independently and at less risk within the home. Motion sensors, medication reminder systems linked to mobile phones, pill compliance detectors, and wireless devices that transmit data on blood pressure and other physiological indicators are just some of the tools being used. These systems can be less costly than assisted living and nursing home care.' - ACM TechNews
  (tags: innovation ubicomp biomedical+informatics)
• How to beat the recession using underutilised technology | 10 Feb 2009 | ComputerWeekly.com
  'Green information technology, social computing platforms, microblogging, cloud computing, and video telepresence are current technologies that are expected to have a transformative impact over the next several years. There also are various emerging technologies that could offer organizations insight into the marketplace's business and innovation potential.'
  (tags: innovation information+technology)
• Unnatural selection: Robots start to evolve - tech - 04 February 2009 - New Scientist
  'As animals evolved, additions of small groups of neurons on top of existing neural structures are thought to have allowed their brain complexity to increase steadily, he says, keeping pace with the development of new limbs and senses. In the same way, Macleod's robot's brain assigns new clusters of "neurons" to adapt to new additions to its body.'
  (tags: robotics evolution ai)
• Cognitive Computing Project Aims to Reverse-Engineer the Mind | Gadget Lab from Wired.com
  'In what could be one of the most ambitious computing projects ever, neuroscientists, computer engineers and psychologists are coming together in a bid to create an entirely new computing architecture that can simulate the brain's abilities for perception, interaction and cognition. All that, while being small enough to fit into a lunch box and consuming extremely small amounts of power.'
  (tags: ibm cognitive+psychology)
• TheRecord.com - Business - Software analyzes medical images while 'thinking' like a doctor
  'University of Waterloo researchers led by professor Hamid Tizhoosh have developed Segasist, software that can analyze medical images to identify tumors, lesions, and other objects. Tizhoosh says his team merged years of research on artificial intelligence with the field of medical imaging to create a program that can learn from a doctor's biases and preferences until it can think like that doctor when analyzing an image.' -ACM TechNews
  (tags: biomedical+informatics)

links for 2009-02-14

• caBIG Data Sharing and Intellectual Capital Knowledge Center Wiki
  'The caBIG® Data Sharing and Intellectual Capital (DSIC) Knowledge Center is an NCI-supported entity led by the University of Michigan. The DSIC Knowledge Center provides a centralized, authoritative repository of processes, model agreements, and other resources to encourage and facilitate data sharing to advance scientific discovery, consistent with applicable legal, regulatory, ethical and contractual requirements.'
  (tags: physio-mimi)
• RxNav
  'RxNav is a browser for RxNorm, the NLM repository of standard names for clinical drugs. RxNav displays links from clinical drugs, both branded and generic, to their active ingredients, drug components and related brand names. RxNorm is one of a suite of designated standards for use in U.S. Federal Government systems for the electronic exchange of clinical health information.'
  (tags: physio-mimi)

links for 2009-02-13

• UMLSKS: Home
  UMLS Knowledge Source Server
  (tags: physio-mimi UMLS)
• An integrated informatics infrastructure for pre-clinical research-it support
  'This dissertation introduces a Multi-modality Multi-resource Information Integration (MIMI) system that combines scientific and administrative support in a seamlessly integrated environment. MIMI captures a complete set of raw information about people, projects, resources, materials, accounting, scheduling, and scientific data. It replaces the existing piece-meal and disintegrated approach to research-IT support by a single comprehensive package. No other system in the market today provides such a complete set of features to meet the informatics infrastructure challenge. MIMI is created from object-oriented data models that represent the flow of information at core facilities and capture a high-level view of their daily operations.'
  (tags: physio-mimi)
• MIMI: Multimodality, Multiresource, Information In...[J Digit Imaging. 2007] - PubMed Result
  'To address these [scientific and administrative] informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment.'
  (tags: physio-mimi)
• User:Mafs/RSS - Meta
  Tool for embedding external RSS feeds in a MediaWiki wiki.
  (tags: physio-mimi)
• CWRU CTSA Biomedical Research Information Management Program
  'One significant practical challenge encountered by high throughput proteomics facilities is the efficient utilization of costly instrumentation, computing facilities, software and staff time as well as the storage and archiving of large volumes of experimental data and results. Such challenges only become more magnified as facilities grow and new techniques and tools require increased knowledge and produce increasing volumes of data. There are no off-the-shelf software packages which combat these challenges adequately. In order to combat these challenges, the Case Center for Proteomics has collaborated with the Department of Electrical Engineering and Computer Science in the Case School of Engineering to develop a comprehensive web-based center management system.'
  (tags: physio-mimi)
• Clinical & Translational Science Collaborative
  'The ultimate goal of the Clinical & Translational Science Collaborative in Cleveland, directed by Pamela B. Davis, M.D., Ph.D. and Richard A. Rudick, M.D., is to provide complete service and integrated clinical translational research capability within the Cleveland community that will improve the health of patients in Northeast Ohio through patient-based research.'
  (tags: physio-mimi CTSA)
• CCI - Research Informatics Core
  'The CCI's Research Informatics Core (RIC) is the technology and programming heart of the Center for Clinical Investigation. The aim of the RIC is to develop and make available informatics systems and tools that support each step of the scientific process. This aim is guided by the philosophy that well-organized and structured research data allow for greater analytic efficiency and accuracy and pave the way for meaningful scientific discovery. '
  (tags: physio-mimi)
• CCI - Center for Clinical Investigation
  'The mission of the CCI is to enhance clinical and translational research efforts across the Cleveland area, spurring advances in knowledge of risk factors, outcomes and treatment effectiveness in the population, facilitating the transfer of scientific advances to the community, and developing a new generation of clinical researchers equipped with the skills needed to efficiently design, implement and interpret novel studies that address important public health questions. '
  (tags: physio-mimi)
• Case Center for Imaging Research
  'Case Center for Imaging Research, a joint venture between Case Western Reserve University School of Medicine and University Hospitals of Cleveland, extends the strategies that have led to successes in bringing novel imaging technologies to the CWRU campus, expands interdepartmental collaboration and interdisciplinary research and facilitates CWRU’s becoming an emerging leader in imaging research. The center also creates the requisite regional intellectual and instrumentation infrastructure to allow interdisciplinary teams to grow to the next level of success, and lead to new synergies and interactions for development of additional future interdisciplinary research groups.'
  (tags: physio-mimi)
• Magpie RSS - PHP RSS Parser
  For embedding RSS in a PHP page; intend to use for MediaWiki.
  (tags: rss mediawiki)
• Physio-MIMI project wiki
  Need to log in to use the wiki.
  (tags: physio-mimi wiki)
• Help:Properties and types - semantic-mediawiki.org
  'Properties and types are the basic way of entering semantic data in Semantic MediaWiki. Properties can be viewed as «categories for values in wiki pages». They are used by a simple mark-up, similar to the syntax of links in MediaWiki...'
  (tags: physio-mimi)
• Online ICD9/ICD9CM codes
  Free online searchable 2009 ICD-9-CM
  (tags: physio-mimi ontology icd9 icd-9-cm coding)

links for 2009-02-08

• News ArticleGP software 'to prevent heart disease'
  'New computer software that will allow GPs to more accurately assess which patients are most at risk of developing heart disease has been released for clinical use.

  QRISK2 uses a new cardiovascular disease (CVD) equation to estimate an individual’s risk of developing the heart condition over the next 10 years and draws on analysis of 15 years’ worth of real primary care data from the UK.'

  
  
  (tags: health+IT health+informatics biomedical+research clinical+research)
  
  
• 
  
  Hospitals with better IT have fewer deaths, study shows
  
  
  'The level of technology deployed by hospitals to help doctors and nurses automate their work can mean the difference between life and death, according to a recently reported study. The study, involving more than 167,000 patients in 41 hospitals, also showed that better IT lowered costs.'
  
  
  (tags: health+IT health+informatics biomedical+research clinical+research)
  
  

links for 2009-02-04

• 01.28.2009 - Improved method for comparing genomes as well as written text
  'The new method can be used to compare even distantly related organisms or organisms with genomes of vastly different sizes and diversity, and can compare the entire genome, not just a selected small fraction of the gene-containing portion known to code for proteins, which in the human genome is only 1 percent of the DNA. The technique produces groupings of organisms largely consistent with current groupings, but with some interesting discrepancies, according to Sung-Hou Kim, professor of chemistry at UC Berkeley and faculty researcher at Lawrence Berkeley National Laboratory. However, the relative positions of the groups in the family tree - that is, how recently these groups evolved - are quite different from those based on conventional gene alignment methods.'
  (tags: bioinformatics genomics biomedical+informatics biomedical+research natural+language+processing)

Natural language processing: the key to the *omics revolution?

I wasn't the first (or the brightest) informatics geek to notice the similarity between the molecular structures of the various *omics diciplines and the concept of the textual corpus. A number of researchers here at Michigan are applying linquistic techniques in systems biology, so there's a natural curiosity about that similarity on my part, even if it's not where I spend my time.

Last week I came across a, dare I say, "textbook" example of the use of natural language processing (NLP) to advance genomics, in a news release from UC Berkeley entitled Improved method for comparing genomes as well as written text. Here's a fairly large taste:

Taking a hint from the text comparison methods used to detect plagiarism in books, college papers and computer programs, University of California, Berkeley, researchers have developed an improved method for comparing whole genome sequences.

With nearly a thousand genomes partly or fully sequenced, scientists are jumping on comparative genomics as a way to construct evolutionary trees, trace disease susceptibility in populations, and even track down people's ancestry.

To date, the most common techniques have relied on comparing a limited number of highly conserved genes - no more than a couple dozen - in organisms that have all these genes in common.

The new method can be used to compare even distantly related organisms or organisms with genomes of vastly different sizes and diversity, and can compare the entire genome, not just a selected small fraction of the gene-containing portion known to code for proteins, which in the human genome is only 1 percent of the DNA.

The technique produces groupings of organisms largely consistent with current groupings, but with some interesting discrepancies, according to Sung-Hou Kim, professor of chemistry at UC Berkeley and faculty researcher at Lawrence Berkeley National Laboratory. However, the relative positions of the groups in the family tree - that is, how recently these groups evolved - are quite different from those based on conventional gene alignment methods.

The computational results have surprised scientists in being able to classify some bacteria and viruses that until now were enigmatic.

The real deal has appeared online in the Proceedings of the National Academy of Sciences; here's the citation:

Gregory E. Sims, Se-Ran Jun, Guohong A. Wu, and Sung-Hou Kim, "Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions", PNAS: published online before print February 2, 2009, doi:10.1073/pnas.0813249106

I can't say I'm intimately familiar with the feature frequency profiles concept, but then I'm an NLP buff rather than an expert.  The link above takes you to a page where you can download the preprint as a PDF, which has a few typos, but gives a fairly clear grad-student-reading-level description of the algorithm and how they optimize it for particular genomes. Cool stuff!

I'm not sure how directly this will apply to other *omics disciplines, such as proteomics and metabolomics, which are where much of the real action is found in biomedical research. Still, it's an exciting development, and a harbinger of things to come, as the NLP community takes on the challenge of the greatest story ever told, the story of life as viewed through the lens of molecular biology.