Celebrating One Million Records: An Open-access Database for Clinical Geneticists (Technology Networks)

Technology Networks: Celebrating One Million Records: An Open-access Database for Clinical Geneticists . “ClinVar has announced the submission of the one-millionth record to its open-access database. The millionth submission was published on Friday, December 20, 2019, a milestone achievement for providing open access to human variant data with asserted consequences to the clinical genetics and research communities.”

Phys .org: Turning a handheld smartphone into a fluorescence microscope

Phys .org: Turning a handheld smartphone into a fluorescence microscope. “Researchers in the U.S. and China have developed a method to transform a smartphone into a fluorescence microscope. The handheld smartphone-fluorescence microscope (HSFM) device allows complex biomedical analyses both rapidly and inexpensively.”

Phys .org: New tool mines scientific texts for fusion protein facts

Phys .org: New tool mines scientific texts for fusion protein facts. “Different kinds of fusion proteins can arise naturally in the human body, sometimes leading to cancer. Understanding interactions between fusion proteins and other proteins can help improve personalized cancer treatment. However, the number of scientific papers discussing these interactions is growing rapidly, and there is no standard format for presenting this information. Thus, organizing and keeping abreast of this knowledge poses a major challenge.”

Stanford Medical: Stanford to lead development of coordinating hub for biomedical ethics

Stanford Medical: Stanford to lead development of coordinating hub for biomedical ethics. “The Stanford Center for Biomedical Ethics has been chosen by the National Human Genome Research Institute to help lead the development of a coordinating hub for information on the ethical, legal and social implications of genetic research.”

University of Alberta: First global open-source database for spinal cord injury research will be a ‘game-changer,’ say experts

University of Alberta: First global open-source database for spinal cord injury research will be a ‘game-changer,’ say experts. “Experts from the University of Alberta and two universities of California are teaming up to launch the world’s first open-source database for spinal cord injury research. The Open Data Commons for preclinical Spinal Cord Injury research (ODC-SCI) will improve research and treatment worldwide by making data more accessible, according to researchers and patients.”

Science: In departure for NIH, Cancer Moonshot requires grantees to make papers immediately free

Science: In departure for NIH, Cancer Moonshot requires grantees to make papers immediately free. “The long-standing debate over open access to research results has been marked by a geographic divide. In Europe, some public funders have launched a high-profile open-access initiative, dubbed Plan S, that would ultimately require grantees to publish only in journals that immediately make papers free to all. But in the United States, federal agencies have stuck to a decade-old policy that allows grantees to publish in journals that keep papers behind a paywall for up to 1 year. Now, the divide is starting to blur, with one prominent U.S. research program starting to require immediate open access to the peer-reviewed publications it funds.”

TechXplore: Reconstructing histological slices into 3-D images

TechXplore: Reconstructing histological slices into 3-D images. “Despite advances in 3D imaging such as MRI and CT, scientists still rely on slicing a specimen into 2-D sections to acquire the most detailed information. Using this information, they then try to reconstruct a 3-D image of the specimen. Researchers from Nara Institute of Science and Technology report a new algorithm that can do this task at less cost and higher robustness than standard methods.”

WESA: All Of Us Research Study, With Goal To Recruit 1 Million Participants, Turns 1 Year Old

WESA: All Of Us Research Study, With Goal To Recruit 1 Million Participants, Turns 1 Year Old. “A massive National Institutes of Health study with a recruitment hub in Pittsburgh has turned a year old. The All of Us precision medicine project has an aim to recruit 1 million people, and it still has a long way to go. The goal is to assemble a vast database for future research studies, with more than half the pool coming from diverse ancestral backgrounds, and including sexual and gender minorities.”

IDEALS @ Illinois: How comprehensive is the PubMed Central Open Access full-text database?

IDEALS @ Illinois: How comprehensive is the PubMed Central Open Access full-text database? (this link goes to a PDF.) “The comprehensiveness of database is a prerequisite for the quality of scientific works established on this increasingly significant infrastructure. This is especially so for large-scale text-mining analyses of scientific publications facilitated by open-access full-text scientific databases. Given the lack of research concerning the comprehensiveness of this type of academic resource, we conducted a project to analyze the coverage of materials in the PubMed Central Open Access Subset (PMCOAS), a popular source for open-access scientific publications, in terms of the PubMed database. The preliminary results show that the PMCOAS coverage is in a rapid increase in recent years, despite the vast difference by MeSH descriptor.”

New York Times: Making New Drugs With a Dose of Artificial Intelligence

New York Times: Making New Drugs With a Dose of Artificial Intelligence. “You can think of it as a World Cup of biochemical research. Every two years, hundreds of scientists enter a global competition. Tackling a biological puzzle they call ‘the protein folding problem,’ they try to predict the three-dimensional shape of proteins in the human body. No one knows how to solve the problem. Even the winners only chip away at it. But a solution could streamline the way scientists create new medicines and fight disease.”

The web meets genomics: a DNA search engine for microbes (EurekAlert)

EurekAlert: The web meets genomics: a DNA search engine for microbes . “The search engine, called Bitsliced Genomic Signature Index (BIGSI), fulfils a similar purpose to internet search engines, such as Google. The amount of sequenced microbial DNA is doubling every two years. Until now, there was no practical way to search this data. This type of search could prove extremely useful for understanding disease. Take, for example, an outbreak of food poisoning, where the cause is a Salmonella strain containing a drug-resistance plasmid (a ‘hitchhiking’ DNA element that can spread drug resistance across different bacterial species). For the first time, BIGSI allows researchers to easily spot if and when the plasmid has been seen before.”

Phys .org: Researchers develop tool that analyzes biomedical data within minutes

Phys .org: Researchers develop tool that analyzes biomedical data within minutes. “Researchers at the Icahn School of Medicine at Mount Sinai have developed a tool that speeds up the analysis and publication of biomedical data from many months or years to mere minutes, transforming the way researchers communicate results of their studies. Until now, the primary method available to share biomedical research data has been through print publication in scientific journals. The new tool, BioJupies, relies on cloud technologies to analyze and visualize large amounts of data, such as that acquired by genome sequencing, as described in the November 2018 issue of Cell Systems.”

NIH: NIH makes STRIDES to accelerate discoveries in the cloud

NIH: NIH makes STRIDES to accelerate discoveries in the cloud. “The National Institutes of Health has launched a new initiative to harness the power of commercial cloud computing and provide NIH biomedical researchers access to the most advanced, cost-effective computational infrastructure, tools and services available. The STRIDES (Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability) Initiative launches with Google Cloud as its first industry partner and aims to reduce economic and technological barriers to accessing and computing on large biomedical data sets to accelerate biomedical advances.”

PR Newswire: MedGenome Launches Ophthatome Knowledgebase at ARVO 2018 (PRESS RELEASE)

PR Newswire: MedGenome Launches Ophthatome Knowledgebase at ARVO 2018 (PRESS RELEASE). “MedGenome announced the launch of OphthatomeTM Knowledgebase, a database with more than 500,000 clinical phenotype records for ocular research at ARVO 2018, the annual meeting of the Association for Research in Vision and Ophthalmology. Ophthatome Knowledgebase was developed by MedGenome in collaboration with Narayana Nethralaya, a leading specialty eye-care hospital network based in Bangalore, India, and will be demonstrated at the conference April 29 – May 3.”

National Institutes of Health: NIH program to accelerate therapies for arthritis, lupus releases first datasets

National Institutes of Health: NIH program to accelerate therapies for arthritis, lupus releases first datasets .”Datasets characterizing individual cells in rheumatoid arthritis and systemic lupus erythematosus disease tissue from the Accelerating Medicines Partnership for Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Phase I study are now available to the research community. Scientists from across the biomedical research community can access the AMP RA/SLE datasets to explore important research questions about these autoimmune conditions.”