Category Archives: Bioinformatics

AMIA CIS-WG Approves Patient Demographic Interoperability

The American Medical Informatics Association Computer Information Systems Working Group has approved a white paper calling for implementation of basic patient demographic interoperability using IETF vCardDAV across all HIT applications including practice management. Surprisingly this mostly doesn’t exist right now and most have to register and re-register patients basic demographic information manually. It goes to the working group steering committee now for further approval.

Version 2.5 of OpenClinica Electronic Data Capture (EDC) Software Now Available

Akaza Research announces the availability of version 2.5 of OpenClinica, the popular open source clinical trials software. Full press release after the break.

(Cambridge, MA) September 29, 2008: Akaza Research announces the availability of OpenClinica 2.5, the popular open source clinical trials software. This release marks a major milestone for users of OpenClinica by adding a host of features, many of which are designed to better support regulated industry sponsored clinical trials.

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Open Source Clinical Trial Software Gets Attention at DIA Annual Meeting

Open source in clinical research will be the topic of a panel discussion at the upcoming DIA Annual Meeting June 24th in Boston.

Join us for an interesting discussion on open source clinical trial software the DIA Annual Meeting June 24th in Boston. This presentation will evaluate how open, standards-based software can alleviate the challenges of flexibility, interoperability, and cost in regulated clinical research environments. Presenters will discuss the unique advantages and challenges in developing and using open source software for tasks such as electronic data capture, and provide an overview of other open source technologies currently being used in clinical trials.

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Microsoft Healthvault Patient Safety in Question

Connectologist Tim Gee considers patient safety and HealthVault:

Many have criticized HealthVault regarding privacy and security concerns, or perceived limitations of HV as a personal health record (PHR). I suspect that HV is challenged more by the market’s perception of Microsoft’s long running security issues than with any actual shortcomings of that type in HV. And since HV is not a PHR, but rather a “platform,” criticisms about any lack of PHR features is not relevant. One topic I’ve not seen addressed is the safety and effectiveness of the data within HV – and I don’t mean “safety” as in the data is secure from unauthorized access or misuse. I mean “safety” as in the utilization of data stored in HV by other applications won’t result in an unsatisfactory patient outcome, you know, like death or injury.

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OpenClinica Enterprise Selected to Power Clinical Trials by Australian CRO

OpenClinica Enterprise is being adopted to power clinical trials in Australia and New Zeland by Emphron Informatics, a data management and biostatistics contract research organization (CRO). Full press release within.

(Cambridge, MA) August 13, 2007 � Akaza Research, LLC announced today that OpenClinica Enterprise is being adopted by Emphron Informatics, a data management and biostatistics contract research organization (CRO) in Queensland, Australia. Emphron will use OpenClinica Enterprise to help it better manage its customers� clinical trials throughout Australia and New Zealand.

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Bioknoppix and Medical Live CDs

While researching a review article on free/libre and open source in healthcare, I came across some examples of attempts to integrate/bundle GNU/Linux with other health-related applications. I think we have previously mentioned the Care2x/Knoppix tie-up here, but there seem to be several others:
Bioknoppix ( is one interesting looking collection from Puerto Rico, and CDMEDICPACS another. All are summarised on
I would be interested in hearing from anyone who has used any of them or knows more about them.

Use of FOSS in DNA Microarrays

There is an interesting article in Genomics and Proteomics on the dominence of ‘Freeware’ (which is a misnomer in this case, it should say Free/Open Source Software) vs. proprietary software in genomics research: ‘…Whether an academic DNA microarray user is able to use the accompanying software relates to the nature of academic research, Welebob says, and what they are using the software to do. “For academia, researchers are sitting on National Institutes of Health and National Science Foundation grants, and the goal is to get published. To get published, they have to work within very novel space, so they need software packages where they can open the source code and [alter the program] themselves when they need to. They may be doing experiments and experimental designs that are very different than what a commercial package would support, because commercial packages in many ways are built to support more mainstream experimental designs and applications, which represent the largest market.”

PR: Open Source Stem Cell R&D

U.S. BioDefense to Launch Open Source Platform for Rapid Stem Cell Research and Development. Read on for the complete announcement.

City of Industry, CA � January 21, 2005 – U.S. BioDefense, Inc. (OTCBB: UBDF) announced today that it is developing an Open Source Stem Cell Research Platform to leverage the distributed power of open source development. The Open Source Stem Cell Research Platform will allow researchers at Universities, Government Agencies, and Fortune 500 companies to read, distribute, modify and contribute to stem cell and biotechnology research in an efficient and streamlined method. The platform which can be used as an Intranet or online will provide access to bioinformatic tools and serve as a robust utility for the rapid evolution of Stem Cell technology research, development, and commercialization.

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Book Review: Digital Code of Life

Salon is running a book review on Glyn Moody’s “Digital Code of Life” with subheading ‘tells the story of the bioinformatic revolution: The merging of computers and molecular biology’: ‘…Moody’s last book was “Rebel Code: Linux and the Open Source Revolution,” one of the better books to be written about the free software movement. There are some very significant linkages between the free software movement and bioinformatics. Central to both has been the tension between those who want to share their information (or code) and those who want to keep it secret for proprietary commercial advantage. In the world of cutting-edge genetic research this is a hugely controversial issue…’