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Mendels Accountant is featured project at in genetics and bioinformatics , It works on Linux systems and Windows . Mendels Accountant  is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection .   Mendel’s Acc. authors wrote very optimized documentation and manual for users and [...]



NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification . Aims of NeuroML as mentioned on NeuroML website : To create specifications for a language in XML to describe the biophysics, anatomy and network [...]



ePub is an extension format for electronic publications  , it was generated and used for years for Mobile reader as their favorite extension of choice of electronic publications . ePub still the perfect format on the new generation smartphone including iPhone , Android phones so as iPad and Android Tablets . There are many Medical [...]



iPad is becoming the trend of tablets , and yet it’s the future of computer industry and for doctors it becomes they new pocket ( huge pocket ) tool , for Books reading , reference , and search during their practice , in here i am listing the most important 10 iPad apps for doctors [...]



Open source project , built as a research project for IT-support and home-based health care . Publisher / Developers quote : “This is the source repository for a research project regarding IT-support in distributed and home-based health care.The first pilot application is a diabetes followup application. The application uses Semantic Web technology extensively .” Developer [...]



Diabetic patients needs to keep tracking of their blood glucose readings ,  records , managing their medication , diet , food . There are many projects for such tasks , many of them are commercial software , some are free .   1 – Diabetes Pilot : Commercial diabetes management software 39$ – link : Commercial project built also [...]
MedTech and Devices

geek in the lab



Do you think your Lab software is the tool you need?

Over the past years, I got the chance of get in contact with many Laboratory Information Systems (LIS) available in the market.

And when I look back, and try to analyse them from a safe distance I get the feeling that they all have more similarities than differences.

They all share some common goals:

  • spread as far as posible!!!
  • adapt as fast as you can!!!

damn, look like a virus to me!!!

They all try to reach to different types of Labs, try to do different tasks, try to manage different business environments, try to adapt by all means to the circumstances, etc. And to do this they all seem to loose their vertebra.

Sometimes, it is wise to stop and accept that your software is not tailored to manage all the information concerning your lab.

Let me give you an example, a good clinical management software does not have to be a good stock management software.

Maybe your software is great for communications with lab analysers, but maybe it sucks for data mining.

And sooner or later,  the Lab Manager will ask himself why is he carrying this huge, complicated, heavy, not flexible tool, when most of the time he only need a small tool, and only ocasionally he will need ‘the big stuff’.

Surelly he will wonder, “wouldn’t it be nice to modularize my software, use as I need, and hope my ‘modules’ communicate each other nicely?”



Occasionally, every blogger gets into a situation of wondering if he/she should continue to post.

I’ve been in that (in)decisive situation over the past year. Between two house moves, managing family priorities among everything else, this blog has been stalled.

I’ve decided to try to give the blog a new chance.

Hope this is a good decision.



Now that I’m back in the business, I’m trying to keep up to everything that I missed in this last year.

There was a generous reference to my blog, from DarkDaily that I’d like to share with everybody:

Geek in the Lab
Pedro Fonseca has been an IT healthcare specialist for more than 15 years. It is clear while poking through Geek in the Lab that Fonseca is passionate about information technology as it relates to healthcare. “Geek in the Lab” is laid out so that IT professionals can keep up with the latest in healthcare technology, but it is written in a way that is accessible to the laymen. While many similar blogs are full of difficult to understand technical jargon, Fonseca makes sure his blog is easy for all readers to understand. Far from a “How To” advice column, “Geek in the Lab” keeps track of healthcare IT trends and offers observations on how they may impact the big picture. Fonseca’s “Gadget of the Week” gives readers a glimpse of the latest in IT tech.”

Thanks to Robert L. Michel and his team for such kind words and keep the good work.



Year 2009 was a troubled year.

It was necessary to rethink my life priorities.

This blog was placed behind some other issues.

So, as part of my new year’s resolution for 2010, The Geek is back to the Lab!!!

Have lots of subjects to write about, so I’ll start this week ;-)



fs567012In my last post I’ve stated that the login/password is not secure.

Maybe the problem resides not in the ‘technology’ but as many times on the human factor.

In fact, the main problem is not the login/password procedure, but the way you use it.

So,  in order to study my customers passwords, I tried to create several simple rules to determine if the password used by them are easily crackable or not.

I have done this study using data from an hospital, and having a 400 user accounts.

Let me remind that although our software has several rules implemented for password management, we were asked to turn them down. This rules include:

- time validity

- minimum chars used

- time period for using the same password

- among others.

So, the rules I’ve come up with, are 10 very simple and common sense rules:

Rule 1: Verify if the users ever changed the password (12% didn’t, meaning that they still use the original random password assigned to them)

Rule 2: Verify that password is the same than login (4% use password=login)

Rule 3: Verify if the password is the Institution name (1%)

Rule 4: Verify that the password is the Application name (4%)

Rule 5: Verify if the password is the official employee number (14% use their official number, that is published in every institution document)

Rule 6: Verify if the password is between 1900 and 2009 (25% a year like password)

Rule 7: Verify that password is a 4 digit number, not like Rule 5 (5%)

Rule 8: Verify that password is the user first name (2%)

Rule 9: Verify that password is the user last name (1% use last name, although I haven’t tried maid name)

Rule 10: Verify if the password is a portuguese name (3% use Portuguese names, which I suppose to be children names, or wife/husband names)

This simple 10 rules, allowed me to crack 71% of a 400 user accounts password, meaning 284 user accounts.

I suppose that if I apply this rules to the same users on different applications, I would have got similar results, because the crackable passwords were personal data.

“Do you really think your health data is safe?”

Let´s ban login/password NOW!



fs567012I’ve been working in hospital labs for several years, and have followed the IT evolution in this sector. In the beginning, the lab was an isle, and the information was secure for the physical barriers. The network was restricted to the laboratory, and the access to the software wasn’t password protected.

Then, the hospitals began to connect the several ‘islands’, and implementing a centralized infrastructure.

It was the beginning of domains, and the first contact of the user with logins and passwords.

Then, rapiddly there was a proliferation of software, and each one had different logins and passwords. There was administrative software, clinical, image, lab, infection control, then appeared the intranets and portals, and when the user noticed he had more logins and passwords than he could possibly manage and memorize.

One of the first reaction from users was to unify passwords. But then, some of them had time limit, and others did not, and it was an Herculean task to manage all this info.

Some hospitals tried to implement Single Sign On, others tried to ease access through digital id cards. But the most common access control still is Login/Password.

And why should login/password be banned?

Because it is not secure!

To prove this I have made some tests attempting to figure out what the user password was in several databases installed in different hospitals.

The results leave no doubt that this method is not secure. More than 70% of the passwords were broken in the first 10 rules.

On the next post, I’ll describe the tests I made and the results I got.

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MedTech and Devices

Constructive Medicine 2.0

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News and Views

HL7 News; Tools and Resources Update


The 30th Anniversary Standards and Implementation Meeting of the International Healthcare Modelling Standards Development Organisation (IHMSDO) will be held in Beijing, China. IHMSDO's CEO Rasmussen, speaking at the recent HIMSS AsiaPac event in Brisbane, Australia, expects over 1,100 developers, implementers and users to attend. "I expect a similar number to attend by tele-presence, so we will have well over 2000 participants." said Rasmussen. After the recent amalgamation of HL7 with DICOM and IHE, IHMSDO has significantly accelerated e-Health and Telehealth roll-outs globally. IHMSDO will meet 11-16 September 2016 in Beijing, China.


The next Working Meeting, held in San Diego, USA, will be the 25th anniversary of the founding of Health Level 7. During this time, HL7 has grown from a group of US implementers frustrated with an ever-increasing number of point-to-point interfaces to the leading authority for global healthcare IT standards. While the scope of the first standard was limited to administration of patients, diagnostic laboratory reporting and billing, HL7 today covers all areas of healthcare including genomics. The HL7 meeting in San Diego will be held from 11-16 September 2011.


The next Working Meeting of HL7 International, the leading authority for global healthcare IT standards, will be held May 15-20 in Orlando, Florida, USA. More than 50 Work Groups, Committees and Task Forces will meet to progress the HL7 V2.x, CDA, V3 and EHR Standards.


The recent HL7 International standards organisation Working Meeting in Sydney, Australia, was acclaimed by all attending as a great success. Nearly 350 participants from over 25 countries worked January 9-14 in more than 50 Work Groups, Committees and Task Forces to progress the HL7 V2.x, CDA, V3 and EHR Standards. Many commented on the excellent work environment and the spectacular networking cruise on Sydney Harbour! The first Australian Health Informatics Summer School held in the follwoing week attracted over 40 students from the Asia-Pacific region.


Registrations for the next Working Meeting of the HL7 International standards organisation to be held 9-14 January 2011 in Sydney, Australia, are now open. Additional to the meetings of more than 50 Work Groups, Committees and Task Forces to progress the HL7 V2.x, CDA, V3 and EHR Standards, the event provides an extensive range of Courses, Tutorials and Workshops on CDISC, SOA in Healthcare, GS1, IHE, openEHR, etc. that will allow Australians to hear and learn the very latest developments from the global experts and leaders in e-health. An academic Summer School will also be held.


The presentations given at the HL7 International Plenary Meeting held 3-8 October 2010 in Boston, USA, are now available for download. The slides include "Genetics and Genomics in Clinical Medicine" by Raju Kucherlapati and "Personal Genome Project" by George Church, both from the Harvard Medical School. Summaries of the Panel are also available.
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Tech Medicine


I'll be taking a break from Tech Medicine as Healthline redesigns its Health Experts Network. If you're interested in more musings on technology and medicine, here's how to find me:Blog: Info-SnacksTwitter: JoshuaSchwimmerNephrology and Internal Medicine:


Image via CrunchBaseThe first iPad reviews are out, and they're very positive. Here's a selection of the reviews (compiled by MacRumors): David Pogue, New York TimesWalt Mossberg, All Things DAndy Inhatko, Chicago Sun TimesHere's a roundup of recent medical blogs commentary on the iPad: iMedical Apps has a nice review of how 5 medical apps might appear on the iPad, including the Blausten Human...


Image via WikipediaIn November 2009 Hall & Partner published a study sponsored by Google titled "Connecting with Physicians Online." (Here's the webinar on YouTube and here's the PDF of the presentation.) The study's aim was to better understand how physicians use the internet in their clinical practices. As you'd expect from a study sponsored by Google, it was particularly focused on how...


When you type a search query into Google's web search, a feature called Google Suggest will offer searches that other users have typed that are similar to the one you're typing. Sometimes, this can provide an eye-opening view of how the Internet — or at least, the people who search Google — feel about a particular topic. For example, here are the Google suggested searches for "Doctors...


Image by americanlibraries via FlickrSpoiler alert. Atul's Gawandes new book, The Checklist Manifesto, begins and ends with an ocean of blood. Each of these gruesome bookends is a surgical catastrophe which illustrates the major point of the book: how a simple, "unsexy" checklist can improve medical care. Many excellent reviews of The Checklist Manifesto have already been written. (See, for...


The holy grail of resolution is not high definition video, but telepresence — resolution so good it feels like you're looking through a window, not a TV set or a monitor. Resolution so detailed you feel like you are there. The RED Digital Cinema Camera Company offers a new line of high definition video cameras which have gained an enthusiastic following among directors. (For example, Steven...
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MedTech and Devices

Open Healthcare Framework


Version 0.2.1 of STEM is now available! To get the latest version, please see the OHF Downloads page. Builds are available for Windows, Linux, and Mac OS X.New for version 0.2.1 are over 100 bug fixes, additional features and additional built-in Scenarios. The new features include new "Time Series" and "Phase Space" views. The first view plots graphs of the values of disease variables over Matt Davis


In the lines of the last post, we would like to get some community feedback in order to help us better decide on our future plans. We will start to post some polls and post them in the OHF site. We'll publish a note about new polls in the OHF newsgroup, so please pay attention if you wish to influence.The first poll will be about the ultimate question:To be or not to be? That is XDS.b ...Eishay Smithnoreply@blogger.com1


As we are starting to rump up towards the 2008 IHE Connectathon we recognize we're going to have a better manage user community scalability issues.Last year we had a nice small user community with about fifteen ISVs going with us to the Connectathon and few more how used OHF in the NHIN prototypes and other projects.Those where fun days! We gave our emails to everyone and had an open Skype Eishay Smithnoreply@blogger.com1


A team lead by Senthil Nachimuthu (MD, University of Utah) will conduct an Open Source Workshop at AMIA 2007 in Chicago (Nov, 2007). Contributed to the workshop paper where Thomas Jones, Jon Teichrow, Paul Biondich, Cal Collins, Will Ross, and myself.The workshop will include representatives from the open source projects:* Eclipse Open Healthcare Framework* Machine Learning Tools* Mirth* Tolven* Eishay Smithnoreply@blogger.com1


The recent announcement of the of STEM triggered tons of press and blogs articles about STEM and OHF which was great. It lead a significant increase in the web and mailing list traffic.In the IHE front, our user community is helping us a lot to push the word out. I was told by few attendees of the IHE Workshop occurred last week that Jyran Glucky of BlueWare did a lot of OHF promotion.At about Eishay Smithnoreply@blogger.com0


Today IBM officially announced the contribution of the source code and resources for the Spatiotemporal Epidemiological Modeler (STEM) to the Eclipse OHF Project. In conjunction with this announcement, OHF is also pleased to announce that STEM version 0.2.0 Milestone 1 is available for download. Packaged versions of STEM are available for Windows and Linux. For help using STEM, please see the Matt Davis
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MedTech and Devices




Remember the Star Wars scene in which R2D2 projects a three-dimensional image of a troubled Princess Leia delivering a call for help to Luke Skywalker and his allies? What used to be science fiction is now close to becoming reality thanks to a breakthrough in 3D holographic imaging technology developed at the University of Arizona College of Optical Sciences.

A team led by optical sciences professor Nasser Peyghambarian developed a new type of holographic telepresence that allows the projection of a three-dimensional, moving image without the need for special eyewear such as 3D glasses or other auxiliary devices. The technology is likely to take applications ranging from telemedicine, advertising, updatable 3D maps and entertainment to a new level.

The journal Nature chose the technology to feature on the cover of its Nov. 4 issue.


This item caught my eye in the latest ACM TechNews e-newsletter. Loads of possibilities! Wish I had time to speculate more on it, but today is a busy day.



A leading Australian expert in infectious diseases says people who use display iPads and iPhones at Apple stores are risking serious infections and the company should do more to maintain hygiene.


Another good reason to carry that little bottle of Purell® with you when you go to the mall...



While continuing to poke around on the HealthSystemCIO site today (thanks to the Clinical Groupware Collaborative for the pointer, BTW), I came across a very insightful piece from Dan Morreale on the possibility that stand-alone EHRs may be obsolete.

Without a doubt, EHRs play a vital role within our traditional healthcare delivery model, characterized by independent physician practices and well-defined care delivery systems. As the pace of change has accelerated, however, we have to question how well the EHR — as a stand-alone information silo lacking longitudinal context — is able to handle the demands of coordinated delivery models. It’s time to forget and rethink the model.


Essentially, the problem with existing EHRs is that they are a) hospital-centric, and b) payment-oriented.

Hospital centricity means they are targeted at the large enterprise rather than small businesses like most primary care practices and IPAs). An enterprise can impose software on their employees. A small business must have systems that their staff (especially clinicians) find useful, and most EHRs aren't especially useful to primary care providers (PCPs) in the patient encounter.

Nor were they designed to be --  I'm not roasting the EMR community for designing to the requirements of their target market. A PCP's information requirements are very different from those of the specialist or hospitalist dealing with a patient in the hospital for (in most cases) a previously diagnosed condition with a pre-existing plan of care. PCPs deal with often-nebulous complaints that may take more than one visit to pin down into a definitive diagnosis.

Moreover, care planning for the ambulatory patient, especially those with multiple serious chronic conditions, must take many more factors into account than the in-patient setting.  The patient's home- and community-based informal and paraprofessional support network must be taken into account. Those traditional EHRs that capture such information, and not all do, may nonetheless fail to provide timely access to it.

Because the PCP in an ambulatory practice is ordinarily the decision-maker as well as primary beneficiary of the benefits of an EMR system, and because the PCP's business model requires very careful analysis of costs and benefits, health IT in the ambulatory setting is better viewed as "groupware" rather than enterprise IT. Groupware developers must address key challenges in order to develop systems that are worth more than they cost. Disparities in work and benefit, unobtrusive accessibility, and failures of intuition are all too common in groupware applications, leading to failure to achieve critical mass needed to tip the organization into an IT-driven mode of operation.

The traditional EMR's payment orientation is apparent in an information model that uses ICD-9 for diagnoses and CPT for procedures. These are fine for the in-patient world, but don't capture enough clinical detail for the PCP's purposes, especially with respect to nebulous issues and less-than-certain diagnoses that will take time and more visits to clarify.

Emerging multidisciplinary models of care offer the promise of higher quality for patients and reduced costs for the healthcare industry. These new approaches – including patient-centered medical home (PCMH) and accountable care organizations (ACOs) – harness the power of collaboration among primary care providers, specialists, hospitals, health systems, payers and patients to deliver focused, effective and coordinated care.

To fulfill their promise, however, these models require a different toolset than traditionally has been available to the healthcare market. EHRs, while evidence of technological progress in the industry, were designed to support a provider- and hospital-centric approach to care. As such, they are not fully equipped to catapult the industry towards the collaborative strategy preferred today. ACOs, PMHCs and other approaches will rely upon a platform that facilitates collaboration beyond the enterprise and across the community to achieve multidisciplinary care coordination.

In many ways, the initiatives mentioned in the last paragraph are more important to the PCP than Meaningful Use as defined in the HITECH incentives. ACOs and PCMHs have the potential to provide the right kind of incentive for PCPs to adopt health IT. The only thing missing from that long-term picture is a comprehensive, groupware-oriented IT system tailored to the PCP's requirements.



Rather than requiring all eligible providers and hospitals fill out what is generally the same checklist for Meaningful Use, organizations which prove they are achieving outcomes far beyond the norm could qualify right off the bat, suggested National Coordinator for Healthcare IT David Blumenthal, M.D., at the October HIT Policy Committee meeting.


HealthSystemCIO's Anthony Guerra posted a brief report suggesting that maybe there will be different ways to meet the Meaningful Use (MU) criteria. Or maybe different criteria, I can't quite tell from his remarks.

Just what every family practitioner needs right now -- more uncertainty about HITECH! It's not surprising that a wait-and-see approach may be the path of the vast majority in the 2011 first round of MU.

We at Cielo are hard at work on activities leading to MU certification, but we are working hardest on meeting a higher standard, Meaningful Usability.

A primary care provider may find that their newfangled IT system gets in the way of delivering quality care at the same time they are purportedly documenting it. That may be Meaningful Use by HITECH standards, but it's not Meaningful Usability. We are on track to deliver a system that improves the quality of the patient encounter in addition to documenting the improvement for HITCH and other P4P/P4R purposes.

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MedTech and Devices



You may have seen it on the national news. The past few days, much of Western Washington state has been slammed by a series of snow and ice storms.  The snow (one to two feet in some areas) was bad enough.  Today a very unusual ice storm is...(read more)


On our newest episode of Microsoft Health Tech Today , we connect with a prominent physician educator at  University College London .  Professor Peter Hindmarsh is affiliated with University College London’s developmental endocrinology research...(read more)


This week I’ve been in Las Vegas. I traveled here to meet with Microsoft customers and partners at a CES side event called LEAP at the Mandalay Bay Hotel.  I also did a presentation on health industry tech trends for the UnitedHealth Group in their...(read more)


I wanted to pass along this important announcement about the call for nominations for the annual Microsoft Health Users Group (Microsoft HUG) Awards.  Please see below for full details. Call for Nominations It’s that time of year again for the members...(read more)


Last Thursday and Friday I traveled to New York City to participate in an event organized by Virginia Mason Medical Center (VMMC) in Seattle.  The CEO Health Care Summit, held at the Waldorf Astoria Hotel , drew together a select group of business...(read more)


There was a time when telemedicine services could only be provided by very large clinics, academic medical centers or government health organizations.  Telemedicine required big bulky equipment and expensive dedicated landlines or satellite connections...(read more)
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