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Showing posts with label bioinformatics. Show all posts
Showing posts with label bioinformatics. Show all posts
Saturday, June 30, 2018
Sunday, July 31, 2016
Eric Topols's NIH grant for Precision Medicine & Health Informatics Research
I have tried to read Eric Topol's classic books on digital medicine: "The Patient Will See You Now: The Future of Medicine is in Your Hands" and the "Creative Destruction of Medicine: How the Digital Revolution Will Create Better Healthcare" but my local libraries don't seem to carry them. Not in the habit of buying every book I want to read on Amazon. I think Dr. Topol was a keynote at a nearby eHealth conference not long ago. Instead of attending, I subscribed to his Twitter feed which is well worth a look if you are not already inundated with more information feeds than a human could possibly digest in one lifetime.
The biggest news to come from Dr. Topol I may have first read in the San Diego Union Tribune, a news source I normally would never dream of reading, but for various disparate reasons (or algorithms) came to my attention from sundry WWW news sources. In fact I probably first read about it on the good doctors' Twitter posts. Here is the link to the San Diego article, but it soon became apparent that the RSS was broadly distributed internationally. The Scripps Translational Research Institute, where Professor Topol works, just happens to be in San Diego:
http://www.sandiegouniontribune.com/news/2016/jul/06/NIH-scripps-topol/
The NIH doesn't often dole out $120 million grants for research. The last I heard of a grant with that largess was for research on the artificial brain, and I even blogged about that. What I have not blogged about is precision medicine, which is defined well in this NIH Medline Plus article. I am kind of wondering if precision medicine is just a plain English way of saying translational bioinformatics and health informatics all rolled into one.
This research project, that involves tapping into the blood samples, DNA, social media, health apps, sensor data, Big Data analytics and health records of a million volunteers, reminds me of The Canadian Longitudinal Study on Aging. It certainly does bring to mind a classic in health informatics and epidemiologial research - The Framingham Heart Study of 1948 - which is still providing data for researchers. One can only imagine how the data generated from this research will be analyzed sixty years from now. Artificial Intelligence tools like IBM Watson and Alpha Go, which will probably be employed to help the data scientists, are just in the teething stage, compared to what their exponential computer grandchildren will be able to byte off.
The biggest news to come from Dr. Topol I may have first read in the San Diego Union Tribune, a news source I normally would never dream of reading, but for various disparate reasons (or algorithms) came to my attention from sundry WWW news sources. In fact I probably first read about it on the good doctors' Twitter posts. Here is the link to the San Diego article, but it soon became apparent that the RSS was broadly distributed internationally. The Scripps Translational Research Institute, where Professor Topol works, just happens to be in San Diego:
http://www.sandiegouniontribune.com/news/2016/jul/06/NIH-scripps-topol/
The NIH doesn't often dole out $120 million grants for research. The last I heard of a grant with that largess was for research on the artificial brain, and I even blogged about that. What I have not blogged about is precision medicine, which is defined well in this NIH Medline Plus article. I am kind of wondering if precision medicine is just a plain English way of saying translational bioinformatics and health informatics all rolled into one.
This research project, that involves tapping into the blood samples, DNA, social media, health apps, sensor data, Big Data analytics and health records of a million volunteers, reminds me of The Canadian Longitudinal Study on Aging. It certainly does bring to mind a classic in health informatics and epidemiologial research - The Framingham Heart Study of 1948 - which is still providing data for researchers. One can only imagine how the data generated from this research will be analyzed sixty years from now. Artificial Intelligence tools like IBM Watson and Alpha Go, which will probably be employed to help the data scientists, are just in the teething stage, compared to what their exponential computer grandchildren will be able to byte off.
Thursday, May 9, 2013
Consumer health information discoveries
I have been finding a lot of consumer health information websites, both local and international - a whole bunch of them - and I think it all started when I went to the announcement yesterday for the CISCO/McMaster University Professorship in Integrated Health Biosystems, as well as a Research Chair in Bioinformatics. This doesn't have a consumer health informatics label on it, but should have a Big Data one and be a separate post. Patients come into it when data from clinical trials will finally not go to waste but will be cross-linked with research databases to be put to use for medical research. If personal health records ever catch on, and patients consent to have data (whether de-identified or not - but probably de-identified) used for research, this would also be a mine of information as the original vision for PHR was to include genomic records, the intent being the development and perfection of personalized medicine.
This made me think of Dr. Danny Sands who teaches Medical Informatics at Harvard and is working for CISCO. He had a presentation at a conference (AHIC) where I was also delivering my first student paper presentation. Anyway, I read Danny's bio at CISCO which lead me to a blog he participates in called e-patients.net. It has interesting links to the Society for Participatory Medicine, and the Journal of same.
Impressed with that find, I came across by happenstance the meforyou.org website - a website that can cure you. For some reason this site reminded me about some research and journal articles I read, on how intercessory prayer doesn't work scientifically speaking. It is a website inspired by Facebook new media but created by U of San Francisco:
UC San Francisco is the only university exclusively focused on human health. For 150 years, we've tackled the world's most vexing health issues, from diabetes and malaria to AIDS and cancer. We are driven by the idea that when the best minds come together, united by a common cause, great breakthroughs can be achieved. Because we believe it is perhaps the greatest single breakthrough that can be achieved, we have committed ourselves thoroughly to the realization of precision medicine. We began this movement knowing that we could not do it alone, and continue assured that we will do it together. Join us.
And then I found this surprising and local "searchless" health information website - hi - consumerhealthinfo.ca (a URL I wished I could have claimed). You can't not appreciate the layout, and user interface (think old people with no time to read extensively.) I think Dr. Mike Evans ( Dr. Mike Evans curates the best health information found online. ) contributes to this site which lead me to his blog and website, which is simply brilliant, and this viral video!
And finally after this amazing journey just seemed to be beginning, Dr. Evans recommended the ultimate consumer health informatics website NHS.UK I had recently read on a Yahoo website the UK's National Health Service was in the top ten biggest employers in the world! Well, a lot of them were busy preparing this website, and I relish reading their entire medical encyclopedia someday.
This made me think of Dr. Danny Sands who teaches Medical Informatics at Harvard and is working for CISCO. He had a presentation at a conference (AHIC) where I was also delivering my first student paper presentation. Anyway, I read Danny's bio at CISCO which lead me to a blog he participates in called e-patients.net. It has interesting links to the Society for Participatory Medicine, and the Journal of same.
Impressed with that find, I came across by happenstance the meforyou.org website - a website that can cure you. For some reason this site reminded me about some research and journal articles I read, on how intercessory prayer doesn't work scientifically speaking. It is a website inspired by Facebook new media but created by U of San Francisco:
UC San Francisco is the only university exclusively focused on human health. For 150 years, we've tackled the world's most vexing health issues, from diabetes and malaria to AIDS and cancer. We are driven by the idea that when the best minds come together, united by a common cause, great breakthroughs can be achieved. Because we believe it is perhaps the greatest single breakthrough that can be achieved, we have committed ourselves thoroughly to the realization of precision medicine. We began this movement knowing that we could not do it alone, and continue assured that we will do it together. Join us.
And then I found this surprising and local "searchless" health information website - hi - consumerhealthinfo.ca (a URL I wished I could have claimed). You can't not appreciate the layout, and user interface (think old people with no time to read extensively.) I think Dr. Mike Evans ( Dr. Mike Evans curates the best health information found online. ) contributes to this site which lead me to his blog and website, which is simply brilliant, and this viral video!
And finally after this amazing journey just seemed to be beginning, Dr. Evans recommended the ultimate consumer health informatics website NHS.UK I had recently read on a Yahoo website the UK's National Health Service was in the top ten biggest employers in the world! Well, a lot of them were busy preparing this website, and I relish reading their entire medical encyclopedia someday.
Tuesday, April 16, 2013
Brain research projects - no more digital computers or programming!?
There are several huge "artificial brain" research projects going on now. There is one in Israel, United States (biggest NIH research grant in history), and the one in Europe is called the Blue Brain Project. One of the leading directors of the BBP is Henry Markham. I was listening to an interview with him in which he stated that within 10 years, once the virtual brain is created, it will mean computers will no longer need to be programmed - it would mean the end of the line for digital computers! These computers would not need to be programmed because they will have ability to learn by themselves. This really astonishes me. He further stated that the desktop computers in the future will be both digital and artificial brain.
The eHealth implications for the BBP are astronomical. At first the goal of such a virtual brain would be simulations to test drug reactions for Parkinsons or Alzheimers. Of course, those are more translational bioinformatic type of applications, but it would mean that every ordinary computer device would have access to a Dr. Watson type of medical intelligence.
In the spirit of this movement towards neuroscience integration of knowledge and huge research, I am reading Ray Kuzweil's new book "How to Create a Mind: The Secret of Human Thought Revealed". Parts of the book are beyond my ken, especially the chapters describing how the brain grid is constructed and how it works, but I like reading Kurzweil because his theories of the evolution of computers is compelling. Not everyone appreciates the Kuzweil vision, and I found very humorous a review of Kuzweil by Don Tapscott in the Globe and Mail where he quotes a detractor of his writings:
He also has many detractors. Douglas Hofstadter, the Pulitzer Prize-winning author of Gödel, Escher, Bach, once said that Kurzweil's books are “a very bizarre mixture of ideas that are solid and good with ideas that are crazy. It's as if you took a lot of very good food and some dog excrement and blended it all up so that you can't possibly figure out what's good or bad.”I have to return "How to Create a Mind" to the library now, but I almost finished. Can't say I completely understand the "hidden Markov models". I also don't fully agree with Hofstader. Kurzweil even has quotes from Albus Dumdeldore and one of the Weasley clan, and I don't think that detracts from the scholarly work. Many times throughout reading the book I get the feeling that the book was written for both a human and a computer audience. Future "Hals" from 2001 a Space Odyssey are a target audience, and I think this book is a great contribution for computer understanding of human intelligence and how the brain works. br />
Friday, January 25, 2013
Bioinformatics breakthrough - Storing data on DNA
This is a popular story on the news services. It really is a breakthrough for bioinformatics.
For health informatics, I am not so sure it has applications. One benefit of the technology is the "cold storage" of information for long periods of time, because the data is not read or retrieved quickly (yet). Might be a good way to archive medical records.
Shakespeare sonnets encoded in DNA
Genetic code molecules could keep data safe for decades
The Associated Press
Posted: Jan 24, 2013 8:56 AM ET
Last Updated: Jan 24, 2013 6:40 PM ET
Read 65comments65
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(Note:CBC does not endorse and is not responsible for the content of external links.)
The ones and zeroes of digital data were converted into sequences using the four-letter alphabet of DNA. The sequences were then encoded into synthetic strands of DNA. (iStock)It can store the information from a million CDs in a space no bigger than your little finger, and could keep it safe for centuries.
Is this some new electronic gadget? Nope. It's DNA.
The genetic material has long held all the information needed to make plants and animals, and now some scientists are saying it could help handle the growing storage needs of today's information society.
Researchers reported Wednesday that they had stored all 154 Shakespeare sonnets, a photo, a scientific paper, and a 26-second sound clip from Martin Luther King Jr.'s "I Have a Dream" speech. That all fit in a barely visible bit of DNA in a test tube.
COMING UP
Nick Goldman talks to Quirks & Quarks on Jan. 26 at noon on CBC Radio One.
The process involved converting the ones and zeroes of digital information into the four-letter alphabet of DNA code. That code was used to create strands of synthetic DNA. Then machines "read" the DNA molecules and recovered the encoded information.
That reading process took two weeks, but technological advances are driving that time down, said Ewan Birney of the European Bioinformatics Institute in Hinxton, England. He's an author of a report published online by the journal Nature.
DNA could be useful for keeping huge amounts of information that must be kept for a long time but not retrieved very often, the researchers said. Storing the DNA would be relatively simple, they said: Just put it in a cold, dry and dark place and leave it alone.
Ideal for large archives
The technology might work in the near term for large archives that have to be kept safe for centuries, like national historical records or huge library holdings, said study co-author Nick Goldman of the institute. Maybe in a decade it could become feasible for consumers to store information they want to have around in 50 years, like wedding photos or videos for future grandchildren, Goldman said in an email.
Researcher Nick Goldman, shown here holding a vial of DNA, suggests that in a decade, it could become feasible for consumers to use DNA to store information they want to have around in 50 years, like wedding photos or videos for future grandchildren. (European Molecular Biology Laboratory/Nature/Associated Press)The researchers said they have no intention of putting storage DNA into a living thing, and that it couldn't accidentally become part of the genetic machinery of a living thing because of its coding scheme.
Sriram Kosuri, a Harvard researcher who co-authored a similar report last September, said both papers show advantages of DNA for long-term storage. But because of its technical limitations, "it's not going to replace your hard drive," he said.
Kosuri's co-author, Harvard DNA expert George Church, said the technology could let a person store all of Wikipedia on a fingertip, and all the world's information now stored on disk drives could fit in the palm of the hand.
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