By applying some novel algorithms, computational techniques and the innovative programming language Unified Parallel C (UPC) to the cutting-edge de novo genome assembly tool Meraculous, a team of scientists simplified and sped up genome assembly, reducing a months-long process to mere minutes. This was primarily achieved by “parallelizing” the code to harness the processing power of supercomputers.
Broad Institute is teaming up with Google Genomics to explore how to break down major technical...
Fossilized remains of a new bat species, which lived 16 million years ago, walked on four limbs...
Supercomputers have helped scientists find a surprising link between cross-shaped (or cruciform...
Researchers have developed a new approach to studying the effect of multiple genetic variations on different traits. The new algorithm makes it possible to perform genetic analysis of up to 500,000 individuals — and many traits at the same time. Complex models that let you look at the combined action of many different variants have, until now, involved so much computation that it would take a year to run a single complex query.
Dell has announced an extended partnership with TGen to help clinical researchers and doctors globally expand the reach and impact of the world's first FDA-approved precision medicine trial for pediatric cancer. The renewed commitment includes an additional $3 million Dell grant to support continued collaboration with TGen and the Neuroblastoma and NMTRC expanded pediatric cancer clinical trials in EMEA.
Comparing the genomes of different species — or different members of the same species — is the basis of a great deal of modern biology. DNA sequences that are conserved across species are likely to be functionally important, while variations between members of the same species can indicate different susceptibilities to disease. The basic algorithm for determining how much two sequences of symbols have in common is more than 40 years old.
Scientists from the California Academy of Sciences celebrated World Ocean’s Day with a slew of brand new marine discoveries — more than 100 species that are likely new to science. The Philippines is home to the most biologically diverse waters on Earth, and remains the centerpiece of the Academy’s multi-year exploration of the Coral Triangle’s biological treasures.
Advances in technology have generated vast amounts of “omics” data: genomic, epigenomic, transcriptomic, proteomic and metabolomic changes for all types of specimens. Bridging the gap between data generation and investigators’ ability to retrieve and interpret data is essential to realize the biological and clinical value of this wealth of information.
Extracting meaningful information out of clinical datasets can mean the difference between a successful diagnosis and a protracted illness. However, datasets can vary widely both in terms of the number of ‘features’ measured and number of independent observations taken. Now, researchers have developed an approach for targeted feature selection from datasets with small sample sizes, which tackles the so-called class imbalance problem.
In case you missed it, here's another chance to catch this week's biggest hits. Writing like a genius; the largest individual structure ever identified by humanity; imaging fascinating, wild and unpredictable thunder; a car prototype that folds, shrinks and drives sideways; a high-efficiency laser system to remove space debris from orbit; and more are among the latest top stories.
The list of authors for an article on comparative genomics of a fruit fly chromosome runs three single-spaced pages. Large author lists are the norm in high-energy physics, but a novelty in biology. What is going on? The 1,014 authors include 940 undergraduates from 63 institutions, all working in parallel to solve mysteries embedded in the DNA sequences of the unusual dot chromosome in fruit flies. A large collaboration is providing...
IBM Watson is collaborating with more than a dozen leading cancer institutes to accelerate the ability of clinicians to identify and personalize treatment options for their patients. The institutes will apply Watson's advanced cognitive capabilities to reduce from weeks to minutes the ability to translate DNA insights, understand a person's genetic profile and gather relevant information from medical literature to personalize treatment.
The DeskGen Platform for gene editing combines elements of AutoClone and gUIDEbook and allows researchers to design genome editing vectors and cloning strategies optimized to their own laboratories and experimental needs. It provides the power to expertly design optimized genome editing experiments, in any cell line and species, right from the desktop.
Computer Science, Statistical Methods Combine to Analyze Stunningly Diverse Genomic Big Data CollectionsApril 28, 2015 3:36 pm | by Simons Foundation | News | Comments
A multi-year study led by researchers from the Simons Center for Data Analysis and major universities and medical schools has broken substantial new ground, establishing how genes work together within 144 different human tissues and cell types in carrying out those tissues’ functions. The paper also demonstrates how computer science and statistical methods may combine to analyze genomic ‘big-data’ collections.
Cray XC40 will be First Supercomputer in Berkeley Lab’s New Computational Research and Theory FacilityApril 23, 2015 3:17 pm | by NERSC and Berkeley Lab | News | Comments
The U.S. Department of Energy’s (DOE) National Energy Research Scientific Computing (NERSC) Center and Cray announced they have finalized a new contract for a Cray XC40 supercomputer that will be the first NERSC system installed in the newly built Computational Research and Theory facility at Lawrence Berkeley National Laboratory.
The GenomeStack Big Data Analytics platform has been developed specifically for bioinformatics researchers, data scientists and analysts conducting genome research. The database replaces the traditional file-based, manual process for storing and analyzing genome sequenced data.
Technological advances are enabling scientists to sequence the genomes of cancer tumors, revealing a detailed portrait of genetic mutations that drive these diseases. But genomic studies are only one piece of the puzzle that is precision medicine. In order to realize the promise of this field, there needs to be an increased focus on creating robust clinical databases.
Researchers have long believed that supercomputers give universities a competitive edge in scientific research, but now they have some hard data showing it’s true. A Clemson University team found that universities with locally available supercomputers were more efficient in producing research in critical fields than universities that lacked supercomputers.
The decades worth of data collected about the billions of neurons in the brain is astounding. To help scientists make sense of this “brain big data,” researchers at Carnegie Mellon University have used data mining to create a publicly available Web site that acts like Wikipedia, indexing physiological information about neurons. The site will help to accelerate the advance of neuroscience research by providing a centralized resource.
Efficient, Time Sensitive Execution of Next-gen Sequencing Pipelines Critical for Translational MedicineApril 6, 2015 3:26 pm | by Suzanne Tracy, Editor-in-Chief, Scientific Computing and HPC Source | Blogs | Comments
Demand for genomics processing is rapidly spreading from research labs to the clinical arena. Genomics is now a "must have" tool for researchers in areas of oncology and rare diseases. It is also becoming a requirement in the clinical space for precision medicine, translational medicine and similar "bench to bedside" initiatives.
Qlucore Omics Explorer 3.1 for Mac is data analysis software designed to maximize the outcome of research by making it easy to analyze experiment data from a biological point-of-view. Examples of this are the inbuilt Gene Ontology (GO) Browser, a Gene Set Enrichment Analysis (GSEA) function, and freedom to explore data using any variable identifier: variable collapse.
A new study suggests that a novel DNA-peptide structure can be used to produce thin, transparent and flexible screens. The research harnesses bionanotechnology to emit a full range of colors in one pliable pixel layer — as opposed to the several rigid layers that constitute today's screens.
Big data: It’s a term we read and hear about often, but is hard to grasp. Computer scientists tackled some big data about an important protein and discovered its connection in human history as well as clues about its role in complex neurological diseases. Through a novel method of analyzing these big data, they discovered a region encompassing the gephyrin gene on chromosome 14 that underwent rapid evolution after splitting in two...
Fossil remains of a previously unknown species of a crocodile-like "super salamander" that grew as long as a small car and was a top predator more than 200 million years ago have been found in southern Portugal, researchers announced on March 24, 2015. The prehistoric species, which looked like giant salamanders, grew up to six feet in length and lived in lakes and rivers.
The intraterrestrials, they might be called. Strange creatures live in the deep sea, but few are odder than the viruses that inhabit deep ocean methane seeps and prey on single-celled microorganisms called archaea. The least understood of life's three primary domains, archaea thrive in the most extreme environments: near hot ocean rift vents, in acid mine drainage, in the saltiest of evaporation ponds and in petroleum deposits.
A newly discovered crocodilian ancestor may have filled one of North America's top predator roles before dinosaurs arrived on the continent. The "Carolina Butcher" was a nine-foot-long, land-dwelling crocodylomorph that walked on its hind legs and likely preyed upon smaller inhabitants of North Carolina ecosystems, such as armored reptiles and early mammal relatives.
Breakthrough science requires pioneers. People who combine brilliance with courage, even in the face of daunting opposition. The women who paved the way for modern scientific exploration exemplify this spirit; grappling not only with fundamental questions of the universe, but with discrimination and societal constraints that often stripped them of scientific credit.
University of Pittsburgh, Carnegie Mellon University, UPMC Form Alliance to Transform Healthcare through Big DataMarch 17, 2015 2:19 pm | by UPMC | News | Comments
Today’s health care system generates massive amounts of data — electronic health records, diagnostic imaging, prescriptions, genomic profiles, insurance records, even data from wearable devices. Information has always been essential for guiding care, but computer tools now make it possible to use that data to provide deeper insights. Leveraging big data to revolutionize healthcare is the focus of the Pittsburgh Health Data Alliance.
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