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Bioinformatics—Biology meets Big Data

  dan david june 20155The Black Plague killed between 75-200 million people across Eurasia, decimating 30-60% of Europe’s population in less than 10 years. Blamed for the 14th century pandemic were astrological alignments, lepers, Romani and the ‘poisoning of wells by Jews’, of whose population 200 villages were exterminated in retribution. While humans gradually advanced from that era of misguided superstition, it has only been in very recent years that scientific thought, with the aid of powerful computational capabilities, has begun to take on the largest biological questions and to grasp definitive answers. Enter the Age of Bioinformatics.

Paulien Hogeweg and Ben Hesper coined the term Bioinformatics in 1970 to describe the study of information processes in biotic systems. It was the work of Margaret Oakley Dayhoff and Nobel Prize winning biochemist Frederick Sanger, however, that ushered in the era of Bioinformatics with the use of computers to sequence proteins as early as the 1950s. As the relationship between genes and disease became understood and computing tools more advanced, information technology established its place as an indispensible tool of biology.

Fast forward to the 21st century—“The Big Data” era, where high powered computing systems and sophisticated algorithm designs are powering an incredible velocity of data-influenced advancement in every imaginable field. Computer processing speed having reached the practical nexus of “Moore’s Law,” technology tools can now help us quickly analyze and cross reference massive data sets on everything from retail sales to weather patterns.

These advances have not passed over biological science. Human Genome sequencing is complete. Rapid advances in gene-based drug discovery and development are afoot. Scientists use Bioinformatics systems as complex and ingenious as the organic systems they study to extract useful results from terabytes of statistical and visual data, predicting outcomes with never before possible accuracy. The results are promising—In 2014, a gene sequencing enabled therapy appears to have “cured” most trial patients of the congenital “bubble boy” syndrome which perplexed doctors for decades.

Some of the most important research may come in the ongoing effort to cure cancer. Companies like Google backed Flatiron are aiming to collect complex data from treatment of 1 million cancer patients by 2016 in order to arm physicians with enough statistical insight to determine the best treatment option for each individual patient.

From a growth perspective, the Bioinformatics market —estimated at $4.2 billion in 2015 —is poised to reach $13.3 billion by 2020, growing at a 21% CARG. Harvard, Stanford, MIT and other universities offer specialized Bioinformatics Master and PhD degrees.  The market has welcomed more than a dozen highly sophisticated workflow management systems for Bioinformatics, while a constellation of Bioinformatics conferences and professional organizations have popped up in response, all adding to the rapid proliferation and advance of the industry.

Thanks to Bioinformatics, things even look bright for the Black Plague. In 2001 scientists at the aptly named Sanger Center in Cambridge, England finally cracked the complete genome code of Yersinia Pestis—the bacterium behind the pandemic.


Historic Aztec codex enters the digital age with interactive app

B821835977Z.1_20150119163752_000_G151DHE8Q.6_Gallery.jpgWaterloo Region Record

MEXICO CITY — A 16th-century document considered one of the most important primary sources on the Aztecs of pre-Columbian Mexico went digital this month with a new app that aims to spur research and discussion.

The Codex Mendoza is a 1542 illustrated report ordered by Spanish viceroy Antonio de Mendoza that details sources of riches, Aztec expansion and territorial tributes, and chronicles daily life and social dynamics.

The new interactive codex lets users page through the virtual document, mouse-over the old Spanish text for translations into English or modern Spanish, click on images for richer explanations and explore maps of the area.

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Ancient clay seals found in Israel may shed light on biblical era

3798653882.jpgThe findings could indicate that biblical accounts of David and Solomon described real kings rather than the backwater chieftains considered more likely by some archaeologists.

AP - Impressions from ancient clay seals found at a small site in Israel east of Gaza are signs of government in an area thought to be entirely rural during the 10th century B.C., says Mississippi State University archaeologist James W. Hardin.

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Unlocking Scrolls Preserved in Eruption of Vesuvius, Using X-Ray Beams

Salvatore Laporta/Associated Press

Researchers have found a key that may unlock the only library of classical antiquity to survive along with its documents, raising at least a possibility of recovering vanished works of ancient Greek and Roman authors such as the lost books of Livy’s history of Rome.

The library is that of a villa in Herculaneum, a town that was destroyed in A.D. 79 by the eruption of Mount Vesuvius that obliterated nearby Pompeii.

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Margaret Atwood Protests Removal of Nature Words From Oxford Junior Dictionary

14093346445_209b3a58dc_z.jpgIn the spring, at the end of the day, you should smell like broadband?

Since 2007, Oxford University Press has removed the names of at least 30 plants and animals from its Junior Dictionary in favor of modern words like “broadband” or “cut-and-paste”; and although these changes might reflect the inevitable evolution of the English language, Margaret Atwood and 27 other prominent naturalists, writers and media personalities are concerned that omitting the natural world from children’s vocabularies will have dire consequences.

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