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Obama Initiative Leverages Big Data to Explore the Brain

On Tuesday, April 2, President Obama announced a research initiative that has the ambitious goal of “revolutionizing our understanding of the human brain,” according to a White House press release.

Know as BRAIN (Brain Research through Advancing Innovative Neurotechnologies), the initiative is being launched in FY 2014 with an initial budget of about $100 million, a modest amount given the project’s goals.

In short, BRAIN is designed to help researchers find “…new ways to treat, cure, and even prevent brain disorders, such as Alzheimer’s disease, epilepsy, and traumatic brain injury.” Included is support for new technologies that will allow researchers to produce dynamic pictures of the brain that show how individual brain cells and complex neural circuits interact in real time.

This is a foray into Big Data. The initiative will let researchers amass and analyze the data needed to “…explore how the brain records, processes, uses, stores, and retrieves vast quantities of information, and shed light on the complex links between brain function and behavior.”

Among the many public and private organizations involved in the effort are the National Institutes of Health (NIH), the Defense Advanced Research Projects Agency (DARPA), and the National Science Foundation (NSF). NSF in particular is leading the charge in applying the technologies and techniques of Big Data to the initiative.

The National Science Foundation will play an important role in the BRAIN Initiative because of its ability to support research that spans biology, the physical sciences, engineering, computer science, and the social and behavioral sciences,” according to the White House release. “The National Science Foundation intends to support approximately $20 million in FY 2014 in research that will advance this initiative, such as the development of molecular-scale probes that can sense and record the activity of neural networks; advances in ‘Big Data’ that are necessary to analyze the huge amounts of information that will be generated, and increased understanding of how thoughts, emotions, actions, and memories are represented in the brain.”

In a story in Information Week posted the same day, senior editor J. Nicholas Hoover, writes, “On a conference call with reporters after the President’s announcement, National Institutes of Health director Francis Collins said that the brain-mapping initiative might eventually require the handling of yottabytes of data. A yottabyte is equal to a billion petabytes.”

That’s Big Data at its mind-boggling best.

Read the Full Story.


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Big Data – Quality or Quantity?


In this special guest feature, Anchita Magan from [x]cube DATA writes that the element of quality has to be considered in quantifiable data.

Significance of Big Data

The entire cosmos has been turned into an aggregated ocean of Data – structured or unstructured, systematic or unsystematic, useful or useless. This zillion of roughly organized data is needed to be stored, arranged and analyzed so that it can be brought to use by the business houses to evaluate the dimensions of their success as well as their bottlenecks. Whether a CEO or a COO, a Marketing manager or an operations head, an HR Employee or an IT engineer, they all make use of big data analysis for decision making.
 But the valid question that arises is ‘which attribute of big data is more important – Quality or Quantity?’

Importance of Quantity and Relevance of Quality

The term’ big’ itself is closely related with quantity. But extracting qualitative and fruitful data out of the bulk is the important task which is needed to be accomplished for sustainable growth, effective utilization of resources and to answer the present and foreseeable challenges.

Experts says that we analyze only one percent of Data and hence can tap only 1 percent of its potential. But through systematic data analysis of the rest 99% of data, a revolution can be brought in all the sectors of business era – be it retail, healthcare, telecom, financial services or IT.

But it is also observed that without valid evaluation, collecting hoards of data won’t provide the necessary insights into the business.

Application of Big Data in Health Care Industry with reference to Quality and Quantity

With the boom in Internet and communication technology, big data analysis has gained a lot of significance at the vast global stage. It generate insights on the business performance as a whole by evaluating both the internal and external data collected worldwide.
According to a report by McKinsey five areas with maximum big data potential are health care, retail sector, manufacturing industry, public sector and personal location data.

Taking healthcare industry into consideration, which is currently facing major challenges making their services affordable and accessible to all sections of the society and to the remotest of locations. It has been observed that there is an extensive use of health information and health care data which is processed and analyzed to plan, determine and administer the quality of health services and scientific research for major breakthroughs in the fields of diagnosis and medication. The government as well as private organizations provide multiple statistical reports which throw light on the administrative data regarding the expenditure, consumption and utilization of health services, keeping in account the patient’s records, lab records, number of hospitals, bed utilization rates, out-patient visits, occupancy rates, human resources, etc.

This structured and unstructured data can be a guiding light only when it is properly categorized, processed and analyzed to extract the fruitful insights and discarding the useless content, thus turning the quantitative data into a qualitative one. This is achieved through techniques of big data analytics which is a key to the dynamic potential capability of an organization. These big data techniques include text data mining, machine learning and statistical programming, which are backed by widely used technologies like NoSQL databases and Hadoop Framework.

These technologies of big data analysis further helps to control fraud by enabling the auditors to identify the transactions that indicate the activities of artifice or treachery and thus strengthening the anti fraud mechanism of hospitals.

Some applications of big data in healthcare are:

  • By combining the most advanced laboratory diagnostics, imaging systems and healthcare information technology, Healthcare Industry enables clinicians to diagnose disease earlier and more accurately, making a decisive contribution to improving the quality of healthcare
  • The Healthcare big data technology management offers solutions for the entire supply chain under one roof – from prevention and early detection through diagnosis and on to treatment and aftercare.
  • Big data analytics attempts to examine large amount of data emanating from a variety of sources to discover patterns that could be useful in problem solving and decision making.

The best example can be Bumrungrad International hospitals which are effectively using the clinical analytics and Electronic Medical Record (EMR) to deliver better care for its patients, to analyze their needs and to enhance the patients’ satisfaction along with making their service cost effective. The hospital manages patient information utilizing an integrated hospital information system that uses digital radiology systems. A case study by Intel Corporation unveiled that Bumrungrad commissioned the development of a custom total hospital information system to service both the front office and back office, to maximize both safety and efficiency as well as to drastically reduce the potential for medication error.

Thus it is important to understand that the huge amount of big data has to be well examined, reviewed and verified to deduce the useful content; hence adding quality to the quantifiable data.

About the Author

This article was written by Anchita Magan from [x]cube DATA. [x]cube DATA provides big data solutions and services to companies across various industries that wish to harness the large data sets at their disposal and gain actionable insights from it.


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Life Sciences and Big Data: Made for Each Other

You can’t find better examples of the promises and pitfalls of Big Data than in the realm of the life sciences. According to an excellent article, “Unraveling the Complexities of Life Sciences Data,” published in the journal Big Data, with the combination of the completion of the human genome project and the availability of advanced analysis technologies, “the 21st-century life sciences have entered the fourth paradigm of data-enabled sciences and the realm of big data.”

The authors, Roger Higdon, et. al., note that the scale of biological data is increasing exponentially. Sequencing technologies are producing data faster than the growth of computing power predicted by Moore’s Law – a 10,000-fold increase in sequencing as compared to a 16-fold uptick in computational power. This brings the life sciences squarely up against the challenges of the “5 Vs” of big data: volume, veracity, velocity, variety, and value.

The paper details the specific problems facing life sciences researchers and presents a series of solutions for handling the field’s treasure trove of complex life sciences data. Included is an integrated data resource developed by the Kolker Lab; an efficient way to functionally annotate newly sequence genomes and metagenomes; all-versus-all sequence alignments; a platform under development for visualizing complex data; and a plan for community outreach and education in the data-enabled sciences.

It is clear that the life sciences have become big data and data-enabled science,” the authors conclude. “Data-enabled science may have at its core the generation of data in the lab, but transforming the data to knowledge and action to breakthroughs and benefits goes far beyond the lab. The transformation will require massive resources and transdisciplinary collaborative efforts put forth by the scientific community to solve the challenges of big data. The need is urgent and growing, given the issues of data generation outstripping computing power and the lack of reproducibility of research. Organizations like DELSA Global can inform the life sciences community, lead the way for groups like the Kolker Lab to put forth new solutions to big data challenges, and create a new paradigm in the life sciences of cooperation, collaboration, and sharing at every level.

Read the Full Story.


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How Big Data Helps Scientists Ask Bigger Questions

You have to wonder what Albert Einstein would be up to in this era of big data. Writing in Quartz, Gartner analyst Chris Guan notes that in 1905, Einstein, working with just a handful of data points, discovered that light was made up of particles – a breakthrough that completely changed the course of physics.

A few decades later, Erwin Schrödinger derived an equation that explained many of the new ideas in the fledgling field of quantum mechanics; but the processing power to solve the equation wasn’t available at the time.

Today, with affordable supercomputers, cloud computing, and the ability to move massive amounts of data with Hadoop, scientists have the processing power they need to solve even the most intractable problems. Guan cites the example of a University of Wisconsin researcher who created a massive database of stem cells using over a million processing hours. He finished his study in a week for less than $20,000.

In computer science there are two laws, Amdahl’s and Gustafson’s. Amdahl’s shows how much faster a given problem is answered when more processing power is thrown at it,” says Guan. Gustafon’s turns Amdahl’s on its head by defining how big of a problem can be answered, given a fixed amount of time, when more resources are available. In other words, given an hour, what can be solved with more computers vs. with less. Science, like Gustafson suggested, often opts for bigger questions vs. saved time. The ability to translate larger amounts of data into cogent explanations can help remove old barriers from scientific pursuits. In genetic research, that could mean unlocking the causes of diseases, developing new cures, and finding the parts of the genetic blueprint that make us human.”

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Steve Simms on the Data Capacitor II at Indiana University

In this video from SC12, Steve Simms from Indiana University describes a recent upgrade to the Data Capacitor project, a high-speed, high-capacity storage facility for very large data sets. With 5 PB of storage, Data Capacitor II will support big data applications used in computational research. IU partnered with DataDirect Networks to develop Data Capacitor II, which is scheduled to be installed in the IU Data Center in spring 2013.


Also posted in Flash and SSD, HPC, I/O, Research, Storage, Video | Leave a comment

Video: Can Computers Cure Disease?

In this video fro the Discovery Channel, Intel’s John Hengeveld describes how computers are replacing experimentation as a way to proceed down the scientific process of trial and error. Hengeveld wrote here recently about his experiences with a rare form of cancer and how researchers at Berkeley are using Big Data to save lives with the Cancer Genome Atlas.

Our thoughts go out to John, a very brave man indeed.


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Numeddi Big Data Startup Wins Aptails Pharma Deal

Stanford University spinoff NuMedii has landed a deal with Aptalis Pharma to apply its predictive “Big Data” technology. The companies aim to hunt down and advance drugs to combat gastrointestinal ailments and cystic fibrosis, which are two areas of focus at Aptalis. The deal boosts the commercial credentials of NuMedii, building on the startup’s role in a pair of papers last year that showed how its computational method could quickly pair approved and generic drugs with new potential uses against diseases.

NuMedii’s predictive Big Data discovery technology and its preclinical de-risking expertise are a great fit with Aptalis’ proven capabilities in formulation, clinical development and commercialization of new therapeutics,” said Gini Deshpande, PhD, NuMedii’s CEO and co-founder.

In an interview, Deshpande said that the company is hunting for additional deals with specialty pharma groups as well as partnerships that would enable the company to identify new uses for “shelved” compounds no longer in clinical development. Read the Full Story.


Also posted in Business of Big Data, Research, Startups | 1 Comment

Big Data Sensors in Your Blood

Over at the New York Times, Quentin Hardy writes that biological sensor technology will bring the power of Big Data analytics to healthcare providers.

Make no mistake about these companies’ ambitions. “Ultimately, we see ourselves as a part of the healthcare ecosystem,” Amar Kendale, MC10’s VP of market strategy and development, said in an e-mail. In this future, he wrote, “data will need to be shared seamlessly between customers, providers, and payers in order to reduce heathcare costs and simultaneously deliver the best possible care.” Proteus hopes to use anonymized data from its customers to understand health patterns over an entire population, presumably to revolutionize medicine.

Read the Full Story.


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BGI Tackles DNA Big Data Using NVIDIA Tesla GPUs

Today Nvidia announced the world’s largest genomics institute is using GPUs in in pioneering work of affordable personalized medicine. According to the company, BGI has slashed the time to analyze batches of DNA sequencing data from nearly four days to just six hours using a Tesla GPU-based server farm.

We are drowning in the genome data that our high-throughput sequencing machines create every day,” said Dr. Bingqiang Wang, head of high performance computing from BGI. “GPU acceleration of our genome analysis applications enables our scientists to crunch through data and gain insights into bacteria, plants and humans faster than was ever possible. It offers the potential for researchers and healthcare professionals to identify highly effective and affordable individualized medicines and treatments.”

Speedups like this are considered critically important in determining chemical building blocks that make up a DNA molecule. With a goal of $1,000 genome, the genomics industry aims to make DNA clinical diagnostic tests as a practical component of patient care.

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Big Data’s Glory

Juan Enriquez writes that the marriage Big Data and Biodata will enable a new kind of computing life form.

AND BIG DATA is about to get much, much bigger, as we enter an era in which digital data merges with biology. This synthesis of codes takes the abstract world of digits and brings it back into the physical world. We of course know quite a bit about how life is expressed—in the four letters of DNA, in more than 20 amino acids, in thousands of proteins. We can copy life through cloning. Now we are beginning to be able to rewrite life, not just gene by gene, but entire genomes at a time. This is the difference between inserting a single word or paragraph into a Tolstoy novel (which is what biotechnology does) and writing the entire book from scratch (which is what synthetic biology does). It is far easier to fundamentally change the meaning and outcome of a novel, seed, animal or human organ if you write the entire thing.

Read the Full Story.


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