Applied Bimatics - An Informatics & eHealth Blog

I am a clinician with a passion for informatics. This blog is about my eHealth journey exploring interoperability in Electronic Medical Records (EMR/EHR), Patient Safety, Pharmacovigilance, Data Analytics, Clinical Research and Bioinformatics in a clinical context. Comparing Canadian, Indian and Middle Eastern healthcare systems and services. Join our open facebook group here: https://www.facebook.com/groups/clinical.bioinformaticians/


GIT for Doctors & healthcare professionals - I

Read the full series on GIT for doctors here

Type 36 JSDF Arm Suit
Type 36 JSDF Arm Suit (Photo credit: Mechanekton)
GIT for us doctors is an acronym for GastroIntestinal Tract. But the GIT I am going to talk about here has nothing to do with GastroIntestinal tract. Do you have any gut feeling about what it is going to be?

Well, GIT according to wikipedia is a distributed revision control and source code management (SCM) system with an emphasis on speed. What has that got to do with healthcare professionals and doctors? As healthcare is becoming tech savvy, healthcare professionals and some doctors have started to recognize and understand, not just completed software products, but their source code as well.

The rising prominence of open-source movement in healthcare will greatly benefit from this, as doctors start contributing actively to healthcare application design and code. When you contribute code to an open-source project, there should be a mechanism to download what others have done, maintain concurrency as others keep adding things, keep track of what you add along with others who contribute, and finally impress the master with your contribution. This process is much more complex than the conventional version control or keeping track of older version by keeping copies of different stages. So that is where GIT steps in.

My aim is not to teach you the nitty-gritties of GIT, so that you will become a master of versioning systems. GIT can be quite challenging for doctors to understand and use. (Can you believe it: It is generally used as a command line tool). My aim is to make you comfortable enough to understand and use GIT in a user-friendly way so that when open source initiatives like openmrs.org talks about using GIT, you will know what they mean. BTW if you use EMRs but have not heard about openMRS.org, do take a look. Maybe you (like me) will also be enticed by their motto “ Write Code. Save Lives.”
Deutsch: Logo von GitHub
Deutsch: Logo von GitHub (Photo credit: Wikipedia)

I will start with actual steps in the next post. In the meantime, join the facebook of GIT called GitHub. https://github.com. If you feel like following someone checkout this guy ;) https://github.com/dermatologist . Don’t download and install anything as yet. Just register for a new account.

Next, download and install this free ‘windows’ to GIT http://www.sourcetreeapp.com/ from a software company called Atlassian. This (surprisingly not so popular yet!) software will make your first experience with GIT painless, I promise.

Will be back again with more. BTW did I tell you that GIT may be useful for collaborative writing too!? Unfortunately GIT was not around when I wrote this article in a dermatology journal in 2007. http://www.ncbi.nlm.nih.gov/pubmed/18032878

Read the full series on GIT for doctors here

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Electronic Health Records heartbleed

Open Source Media Framework Icon
Open Source Media Framework Icon (Photo credit: Wikipedia)
Finally we presented our ultra small EHR project (TED) on wednesday with the promise of pushing it into GitHub as an open-source project soon. The biggest challenge in small turnkey EHRs is data security and privacy. While we were presenting our project the world was desperately seeking the patch for the Heartbleed bug and CRA Canada shut down its portal to avoid any potential data security breach. We are still not sure about the impact of this bug worldwide. So what exactly is heartbleed and how can it effect the burgeoning open-source revolution in health informatics?

Heartbleed is a bug in a widely used open-source encryption method called openSSL. When two computers are securely connected by this method there is a mechanism for periodic checking of this secure connection. We now know that this process was not secure after all, as there was a flow in this method that made the data in the RAM of the computers potentially visible to intruders. The data in the RAM of the computer at any time is likely to be the most sensitive including information such as passwords. This vulnerability was present for almost 2 years till it was spotted recently. Though the obvious question at this point is, who knew about this vulnerability before, the potential ramifications of heartbleed extends right to the heart of the open-source philosophy in secure software systems such as EHRs.

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About Me

As a Dermatologist and Informatician my research mainly involves application of bioinformatics techniques and tools in dermatological conditions. However my research interests are varied and I have publications in areas ranging from artificial intelligence, sequence analysis, systems biology, ontology development, microarray analysis, immunology, computational biology and clinical dermatology. I am also interested in eHealth, Health Informatics and Health Policy.

Address

Bell Raj Eapen
Hamilton, ON
Canada