Monday, April 21, 2014

Keeping Tabs on DNA Biocomputing Systems

Have you heard of DNA computing, biocomputers, or biomolecular computers before? I've been keeping an eye on progress in this field for almost 20 years. It may finally be time for you to do the same.

Simply put, Biocomputers are an evolving form of computing solutions that use DNA, biochemistry and molecular biology, instead of the traditional silicon-based computer technologies.

The promising field of biomolecular computer research utilizes the science behind nano-sized biomaterials to create various forms of computational devices, which may have many future applications in healthcare.

Biocomputers are still in the research and development stage and have quite a way to go before a range of viable commercial products will emerge. However, DNA computing, or biomolecular computing, has now become a fast developing interdisciplinary area.

Brief Timeline

    • Back in the late 1990's, the first articles began to appear about scientists and researchers who were working on biocomputer systems of the future.
    • The first proof-of-concept using DNA to perform computation was carried out by Professor Leonard Adleman at the University of Southern California in 1994.
    • In 1997, researchers at the University of Rochester developed DNA Logic Gates.
    • In March 2002, NASA Jet Propulsion Lab issued a press release on “Using 'Nature's Toolbox, a DNA Computer Solves a Complex Problem”. It stated that a DNA-based computer had solved a logic problem that no person could complete by hand.
    • In February 2003, National Geographic News published an article on “Computers Made from DNA and Enzymes”, reporting that Israeli scientists had devised a biocomputer that can perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC.
    • In April 2004, an article in Science Daily entitled “Biological Computer Diagnoses Cancer and Produces the Drug” stated that a biomolecular computer had been developed that diagnosed in vitro a form of cancer - and then performed an appropriate medical intervention by producing a biologically active molecule with anti-cancer activity.
    • HPC Wire reported in March 2005 that a new version of a biomolecular computer developed at the Technion-Israel Institute of Technology, composed entirely of DNA molecules and enzymes, could perform as many as a billion different programs simultaneously.
    • In August 2006, CNN Technology reported that scientists at Columbia University and the University of New Mexico had produced a biocomputer system called MAYA-II. The system had a molecular array of YES and AND logic gates made up of 100 DNA circuits.
    • In a May 2007, a Medical News Today article entitled “Scientists Develop Tiny Implantable Biocomputers” reported that researchers at Harvard University and Princeton University had made a crucial step toward building biological computers - tiny implantable devices that can monitor the activities and characteristics of human cells.
    • In 2010, an article in New Scientist reported that DNA-based logic gates which could carry out calculations inside the body had been constructed for the first time. The work finally brought the prospect of injectable biocomputers programmed to target specific diseases into reality.
    • In 2011, the 17th International Conference on DNA Computing and Molecular Programming was held at  the California Institute of Technology (Caltech) in Pasadena, California.
    • In January 2013, researchers were able to store a JPEG photograph, a set of Shakespearean sonnets, and an audio file of Martin Luther King, Jr.'s speech "I Have a Dream" on DNA digital data storage.
    • In March 2013, a team of bioengineers from Stanford University, led by Drew Endy, announced that had created the biological equivalent of a transistor, which they dubbed a "transcriptor". The invention was the final of the three key components necessary to build a fully functional biocomputer.
    • In May 2013, Israeli scientists at the Technion-Israel Institute of Technology created an advanced biological transducer. The machine can manipulate genetic codes, and use the output as new input for subsequent computations.
    • In May 2013, Ehud Keinan of the Technion Schulich Faculty of Chemistry in Israel in cooperation with the Scripps Research Institute in La Jolla, California, designed a novel, synthetic molecular computing device that computes iteratively and produces biologically significant results.  See
    • In 2014, it was reported that a team of researchers at Bar-Ilan University in Israel had successfully demonstrated an ability to use strands of DNA to create a nanobot computer inside of a living creature—a cockroach.  See

    Biocomputers utilizing nanobiotechnology may one day become the most energy efficient, most powerful, and most economical of any commercially available computer. DNA computers the size of a teardrop have the potential to be more powerful than today's most powerful supercomputer.   See

    Other economic benefit of biocomputers lie in the potential of all biologically derived systems to one day self-replicate and self-assemble given appropriate conditions.

    Just as important, biomolecular computing devices could be crucial to developing computers that can interact directly with biological systems and even living organisms. This will have a tremendous potential impact on healthcare in the future.

    Biocomputers in Healthcare
    • Biocomputers could be used to deliver enzymes that break down cells via programmable nanoparticles, or to delivering insulin to tell cells to grow and regenerate tissue at the desired location.
    • Surgery would be performed by putting the programmable nanoparticles into saline and injecting them into the body to seek out remove bad cells and grow new cells and perform other medical work

    Unlike silicon chips, DNA-based computers can be made small enough to operate inside cells and control their activity. “If you can programme events at a molecular level in cells, you can cure or kill cells which are sick or in trouble and leave the other ones intact. You cannot do this with electronics,” says Luca Cardelli of Microsoft's research centre in the U.K.   See


    Biocomputers are at the ‘bleeding edge’ of health information and/or computer technology. Products of this emerging field are still probably 10-15 years away from entering the commercial marketplace.

    At this point, Chief Information Officers (CIO) of healthcare organizations should start to monitor progress of this technology annually, keeping in mind that this technology has tremendous potential down the road.

    Finally, progress might improve if developers utilized open source software and development tools, in addition to providing open access to R&D studies and findings.

    Selected Resources & Links

    Sunday, April 13, 2014

    VistA and other 'Open Source EHR Systems Across Florida and the Caribbean

    The installation and use of 'open source' electronic health record (EHR) systems have continued to spread across Florida and many other islands and nations across the Caribbean.  See the map of healthcare facilities running some variant of the 'open source' VistA electronic health record (EHR) system in this region.

    In the state of Florida, all of the U.S. Department of Veterans Affairs (VA) healthcare facilities are continuing to use the well known, award winning VistA System. VA healthcare facilities (i.e. hospitals, outpatient clinics, nursing homes) using VistA include the:

    • Bay Pines VA Medical Center
    • Boca Raton VA Clinic
    • Bradenton VA Clinic
    • Brooksville VA Clinic
    • Broward County VA Clinic
    • Cape Coral VA Clinic
    • Clermont VA Clinic
    • Daytona VA Clinic
    • Deerfield Beach VA Clinic
    • Delray Beach VA Clinic
    • Eglin VA Clinic
    • Fort Pierce VA Clinic
    • Hollywood VA Clinic
    • Homestead VA Clinic
    • Jacksonville VA Clinic
    • Tampa VA Medical Center
    • VA/DoD Joint Clinic
    • Key Largo VA Clinic
    • Key West VA Clinic
    • Kissimmee VA Clinic
    • Lake City VA Medical Center
    • Lakeland VA Clinic
    • Lecanto VA Clinic
    • Leesburg VA Clinic
    • Marianna VA Clinic
    • Miami VA Clinic
    • Miami VA Medical Center
    • Naples VA Clinic
    • New Port Richey VA Clinic
    • Gainesville VA Medical Center
    • Ocala VA Clinic
    • Okeechobee VA Clinic
    • Orange City VA Clinic
    • Orlando VA Medical Center
    • Palatka VA Clinic
    • Palm Harbor VA Clinic
    • Panama City VA Clinic
    • Pembroke Pines/Hollywood VA Clinic
    • Port Charlotte VA Clinic
    • Saint Augustine VA Clinic
    • Sarasota VA Clinic
    • Sebring VA Clinic
    • St Lucie VA Clinic
    • St. Petersburg VA Clinic
    • Stuart VA Clinic
    • Tallahassee VA Clinic
    • The Villages VA Clinic
    • Vero Beach VA Clinic
    • Viera VA Clinic
    • Zephyrhills VA Clinic
    • West Palm Beach VA Medical Center

    The following are other Federal, State, and local community healthcare facilities in Florida currently using other derivatives of the VistA system, e.g. CHCS, RPMS, OpenVistA, vxVistA, WorldVistA.

    • U.S. Naval Hospital Jacksonville
    • Eglin AFB Medical Facility
    • 325th Medical Group  - Tyndall AFB  
    • U.S. Naval Branch Health Clinic - Key West
    • U.S. Naval Hospital Pensacola
    • 1st Special Operations Medical Group - Hurlburt Field

    In addition, the U.S. Department of Defense (DoD) operates over 100 smaller clinics across the U.S. and around the world that use the AHLTA electronic health record (EHR) system that interacts with the CHCS system.  Many of these facilities are in the VistA Installations GIS Map & Database but only major sites are listed in the above table.

    Caribbean & Central America

    The installation and use of 'open source' electronic health record (EHR) systems have also slowly spread into U.S. Territories and nations across the Caribbean and Central America, e.g. Puerto Rico, U.S. Virgin Islands, Mexico. 

    All of the U.S. Department of Veterans Affairs (VA) healthcare facilities in U.S. Territories across the Caribbean are using the well known, award winning VistA System. VA healthcare facilities (i.e. hospitals, outpatient clinics, nursing homes) using VistA include the:

    • San Juan VA Medical Center
    • Arecibo VA Clinic
    • Guayama VA Clinic
    • Mayaguez VA Clinic
    • Ponce VA Clinic
    • Utuado VA Clinic
    • Saint Croix VA Clinic
    • Saint Thomas VA Clinic

    The following are other Federal, State, and local community healthcare facilities in the Caribbean currently using other derivatives of the VistA system, e.g. CHCS, RPMS, OpenVistA, vxVistA, WorldVistA.

    •  U.S. Naval Hospital Guantanamo Bay, Cuba

    Finally, the Inter-American Development Bank (IDB) issued a report in 2010 entitle "Benefits and Costs of Electronic Medical Records: The Experience of Mexico’s Social Security Institute (IMSS)". It provides a summary of the installation of IMSS VistA in 58 hospitals across Mexico and provides many valuable 'lessons learned' from their efforts to adapt VistA to their environment.

    • VistA installed in 58 IMSS Hospitals in Mexico

    I am still trying to get a more accurate list of all the hospitals in Mexico running VistA to include in the VistA Installations GIS Map & Database. Only a few of the sites have been entered so far.

    See the map of all healthcare facilities running some variant of the 'open source' VistA electronic health record (EHR) system across Florida, the Caribbean, and around the world. 

    Finally, other popular 'open source' EHR systems in use across Florida and the Caribbean include OpenEMR and OpenMRS.

    • It has been estimated that there are more than 5,000 installations of OpenEMR in physician offices and other small healthcare facilities across the U.S. serving more than 30 million patients. Further, conservative estimates by the OpenEMR Organization (OEMR)  indicate that OpenEMR is installed in over 15,000 healthcare facilities around the world, translating into more than 45,000 practitioners using the system serving approximately 90 million patients. 
    • As of 2012, OpenMRS was in use at over 100 facilities in more than 30 countries and had been used to record over 2 million patient records around the world. They have a number of installations in Haiti and Central America. See map of OpenMRS installations.

    Thursday, April 3, 2014

    8th Annual Future of Open Source Survey - 2014

    Black Duck Software and North Bridge Venture Partners just announced the results of their annual Future of Open Source Survey for 2014. A record-breaking 1,240 industry influencers took part in this year’s survey.

    This year’s results point toward the increased strategic role that open source software (OSS) has in today’s enterprises, the crucial function OSS plays in developing new technologies, the growth of first-time developers within the OSS community, and the impact it has on daily life.
    According to Lou Shipley, President and CEO, Black Duck. “Open source has proven its quality and security, and reached a point of widespread democratization and proliferation.
    In particular, the survey revealed the three industries expected to be impacted most by OSS are Education (76%), Government (67%), and Healthcare (45%).
    Survey respondents further reported that the top ten areas where OSS will impact our everyday lives include: 

     Web privacy/security
     Home appliance
     Wearable devices
     Monetary exchange/payments
    When asked what OSS technologies were leading in industry, 63% cited cloud computing & virtualization, 57% said content management, 52% selected mobile technology, and 51% answered security.
    Also, 56% of corporations expect to contribute to more open source projects in 2014, signaling a change in the way enterprises view open source. When asked why they engaged with OSS communities, cost reduction was still the top response (61%), but many corporations (45%) responded that they also did so to gain a competitive advantage.
    The survey shows enterprises now organizing to contribute back more actively; as they realize the importance of open source innovation to jumpstart careers and kickstart projects,” said Michael Skok, general partner at North Bridge Venture Partners. "Further, more new areas like the Internet of Things (IoT), which requires interoperability and extensibility, can only be met by open source initiatives, hence the emergence of new communities such as the AllSeen Alliance."
    Additional Findings
    • 72 percent of respondents chose to use OSS because it provides stronger security than proprietary solutions.
    • Building upon this, 80 percent of respondents reported choosing open source because of its quality over proprietary alternatives.
    • 68 percent of respondents said that OSS helped improve efficiency and lower costs
    • 55 percent also indicated that OSS helped create new products and services
    • 50 percent of enterprises report openly contributing to and adopting open source.
    To see the full results from the 8th Annual Open Source Survey conducted by North Bridge and Black Duck, go to Slideshare and view their presentation on The Future of Open Source .
    Overall, the future looks bright not just for open source software (OSS), but for all things 'open'.  Share your thoughts.