Phys .org: High time to open up ecological research

Phys .org: High time to open up ecological research. “Share the code and data behind the research please. It’s easy, but it will have a major positive impact on progress and trust in science. That is the clear message from a new paper in PLOS Biology. An international team of ecologists found that currently, only about a quarter of the scientific papers in their field publicly shares computer code for analyses. ‘To make the science of ecology more transparent and reproducible, sharing is urgently needed.'”

Phys .org: An open-source data platform for researchers studying archaea

Phys .org: An open-source data platform for researchers studying archaea. “To foster scientific exchange and to advance discovery, biologists in the School of Arts & Sciences led by postdoc Stefan Schulze and professor Mecky Pohlschroder have launched the Archaeal Proteome Project (ArcPP), a web-based database to collect and make available datasets to further the work of all scientists interested in archaea, a domain of life composed of microorganisms that can dwell anywhere from deep-sea vents to the human gut.”

Weaving Indigenous knowledge with scientific research: A balanced approach (Phys .org)

Phys .org: Weaving Indigenous knowledge with scientific research: A balanced approach. “Indigenous knowledge, including oral histories, mythologies, place names and classification schemes, can span many generations, preserving information that has helped native communities adapt to natural hazards as well as gradually changing conditions. Although Western scientists have historically deemed such information unreliable, during the past decade there has been increasing recognition of the advantages of bicultural approaches to scientific research, including demonstration of reliability.”

Salesforce: Salesforce Research Develops New Search Engine to Support the Fight Against COVID-19

Salesforce: Salesforce Research Develops New Search Engine to Support the Fight Against COVID-19. “Searching scientific publications requires different techniques from traditional keyword-matching search engines. It’s critical that a COVID-19 search engine interpret the proper meaning in a given search, going beyond finding results based on the frequency with which words appear in documents. And with long documents, it’s valuable to quickly surface relevant passages in search results. COVID-19 Search addresses this by combining text retrieval and NLP — including semantic search, state of the art question answering, and abstractive summarization — to better understand the question and surface the most relevant scientific results.”

CNBC: Why the buzz around DeepMind is dissipating as it transitions from games to science

CNBC: Why the buzz around DeepMind is dissipating as it transitions from games to science. “DeepMind’s army of 1,000 plus people, which includes hundreds of highly-paid PhD graduates, continues to pump out academic paper after academic paper, but only a smattering of the work gets picked up by the mainstream media. The research lab has churned out over 1,000 papers and 13 of them have been published by Nature or Science, which are widely seen as the world’s most prestigious academic journals.”

Emory University: Rollins Launches CoCites, a Radical New Scientific Search Tool

Emory University: Rollins Launches CoCites, a Radical New Scientific Search Tool. “Searching scientific literature is inefficient and ineffective. A complete search on a topic requires an extensive query that combines all relevant keywords and their synonyms. A simple search retrieves only part of the relevant literature depending on the keywords that are searched. With CoCites, users don’t enter keywords, they enter or select the title of the article for which they would like to find related content. The tool retrieves these other articles through co-citations. Articles that are frequently cited together with the selected paper appear at the top of the search results.”

EurekAlert: Microbiome search engine can increase efficiency in disease detection and diagnosis

EurekAlert: Microbiome search engine can increase efficiency in disease detection and diagnosis. “Big data makes big promises when it comes to providing insights into human behavior and health. The problem is how to harness the information it provides in an efficient manner. An international team of researchers has proposed a microbiome search-based method, via Microbiome Search Engine (MSE), to analyze the wealth of available health data to detect and diagnose human diseases.”

University World News: Hunt for coronavirus cure is making science more open

University World News: Hunt for coronavirus cure is making science more open. “…while cities are locked down and borders are closed in response to the coronavirus outbreak, science is becoming more open. This openness is already making a difference to scientists’ response to the virus and has the potential to change the world. But it’s not as simple as making every research finding available to anyone for any purpose. Without care and responsibility, there is a danger that open science can be misused or contribute to the spread of misinformation.”

MIT Technology Review: Over 24,000 coronavirus research papers are now available in one place

MIT Technology Review: Over 24,000 coronavirus research papers are now available in one place.”The news: Today researchers collaborating across several organizations released the Covid-19 Open Research Dataset (CORD-19), which includes over 24,000 research papers from peer-reviewed journals as well as sources like bioRxiv and medRxiv (websites where scientists can post non-peer-reviewed preprint papers). The research covers SARS-CoV-2 (the scientific name for the coronavirus), Covid-19 (the scientific name for the disease), and the coronavirus group.”

Column: COVID-19 could kill the for-profit science publishing model. That would be a good thing (Los Angeles Times)

Los Angeles Times: Column: COVID-19 could kill the for-profit science publishing model. That would be a good thing. “Of all the ways the current coronavirus crisis has upended commonplace routines — such as disrupting global supply chains and forcing workers to stay at home — one of the most positive is how it demonstrates the value of open access to scientific research. Ferreting out a silver lining in an event that has produced the infection of more than 90,000 individuals and taken the lives of more than 3,000 — and is certain to wreak further destruction before it is quelled — is a delicate matter.”

JSTOR Daily: An Epidemic of Retractions

JSTOR Daily: An Epidemic of Retractions. “Nicolas Chevassus-au-Louis’s new book, Fraud in the Lab: The High Stakes of Scientific Research (translated by Nicholas Elliott) tackles the issue of scientific fraud head-on, with some tough love for the scientific community. The book should be read by everyone interested in the sciences. Chevassus-au-Louis offers a welcome reminder that scientists are human, too, subject to the temptations of ambition, to career pressures, and to plain old greed.”

Frontiers in Ecology and the Environment: Quantifying the contribution of citizen science to broad‐scale ecological databases

Frontiers in Ecology and the Environment: Quantifying the contribution of citizen science to broad‐scale ecological databases. “Ecological research increasingly relies on broad‐scale databases containing information collected by personnel from a variety of sources, including government agencies, universities, and citizen‐science programs. However, the contribution of citizen‐science programs to these databases is not well known. We analyzed one such database to quantify the contribution of citizen science to lake water‐quality data from seven US states.”

EurekAlert: New database enhances genomics research collaboration

EurekAlert: New database enhances genomics research collaboration. “The MaveDB database is a repository for data from experiments – called multiplex assays of variant effect (MAVEs) – that systematically measure the impact of thousands of individual sequence variants on a gene’s function. These experiments can provide valuable information about how proteins produced by that gene function, how variants in that gene may contribute to disease, and how to engineer synthetic versions of naturally occurring proteins that are more effective than the original protein.”

Computing: Kew Gardens plans to digitise and release Darwin’s data

Computing: Kew Gardens plans to digitise and release Darwin’s data . “Kew Gardens is planning to implement an integrated collections management system to unify its disparate databases and make their data available to the world. Whilst most think of the sculpted gardens when they think of Kew, and as a plot of land which is home to over 30,000 trees that’s unsurprising, most are unaware that it’s also a centre of scientific research, and home to the world’s most extensive botanic collections.”