Article: Zymo Research Releases Open-Source Bioinformatics Pipeline for SARS-CoV-2 Variant Detection in Wastewater

Open Decision-Support, Research

Zymo Research Releases Open-Source Bioinformatics Pipeline for SARS-CoV-2 Variant Detection in Wastewater

Zymo Research has released the VirSieve Bioinformatics Pipeline source code to the environmental microbiology community to promote global collaboration and support for the detection of SARS-CoV-2 variants in wastewater.

VirSieve is an automated computational pipeline that analyzes sequencing reads from the SARS-CoV-2 virus in wastewater samples to better understand viral variants present in monitored communities. By rating the confidence interval in observed viral mutations, the software has the potential to significantly increase the accuracy of analyzing any changes in the viral genetic material.

Read Full Article

Article: Open-Source COVID-19 ML Datasets; Models; Tools for Data Scientists

Access, Document, Open Decision-Support, Open Health, Research

Open-Source COVID-19 ML Datasets; Models; Tools for Data Scientists

As Covid-19 has impacted almost all countries, data scientists and researchers have come up with different predictive models to predict the spread of disease so that it can help the respective governments to come up with suitable plans and policies to curb the spread.

In this context, it becomes essential for data scientists and analysts to know the most popular and useful models that have been proposed as an outcome of the research, as well as get familiar with different datasets available on the internet.

Read Full Article

Article: What’s peer review? 5 things you should know before covering research

Access, Document, Open Decision-Support, Research

What’s peer review? 5 things you should know before covering research

As scholars and other experts rush to release new research aimed at better understanding the coronavirus pandemic, newsrooms must be more careful than ever in vetting the biomedical studies they choose to cover. One of the first steps journalists should take to gauge the quality of all types of research is answering this important question: Has the paper undergone peer review?

Peer review is a formal process through which researchers evaluate and provide feedback on one another’s work, ideally filtering out flawed and low-quality studies while strengthening others. Academic journals generally do not publish papers that have not survived the process.

Read Full Article

Article: Why some researchers oppose unrestricted sharing of coronavirus data

Access, Document, Open Decision-Support, Research

Why some researchers oppose unrestricted sharing of coronavirus data

“I was up all last night,” says Nnaemeka Ndodo, a molecular bioengineer at the Nigeria Centre for Disease Control (CDC) in Abuja. He sequences coronavirus genomes during the day, and then analyses and uploads the results to an online database at night, working tirelessly alongside his colleagues. “We don’t know Saturday, we don’t know Sunday,” he says.

Researchers around the world are racing to spot variants of the coronavirus SARS-CoV-2 so that they can determine whether the mutated viruses will evade vaccines or make COVID-19 deadlier. Like many scientists, Ndodo shares SARS-CoV-2 genome sequences in a popular data repository, GISAID, that requires users to sign in and to credit those whose data they analyse.

Read Full Article

Article: Health research council moves to mandate immediate open access

Access, Document, Open Decision-Support, Research

Health research council moves to mandate immediate open access

Australian council releases discussion paper on immediate open-access publication of research it funds Australia’s National Health and Medical Research Council has proposed that immediate open-access publication of research resulting from its grants should become mandatory.

The council already requires researchers to list their patents on the government’s SourceIP website, but its existing policy allows a 12-month delay to open-access publication of NHMRC-funded research. The proposed reforms would involve researchers publishing in open repositories, circumventing publishers’ fees, as well as publishing in traditional journals. Authors would be required to retain the rights to publish and share their work. It would also encourage researchers to release non-peer-reviewed preprints.

Read Full Article

Article: Reactive, reproducible, collaborative: computational notebooks evolve

Document, Free, Libre, Open Software, Research

Reactive, reproducible, collaborative: computational notebooks evolve

This year marks ten years since the launch of the IPython Notebook. The open-source tool, now known as the Jupyter Notebook, has become an exceedingly popular piece of data-science kit, with millions of notebooks deposited to the GitHub code-sharing site.

Computational notebooks combine code, results, text and images in a single document, yielding what Stephen Wolfram, creator of the Mathematica software package, has called a “computational essay”. And whether written using Jupyter, Mathematica, RStudio or any other platform, researchers can use them for iterative data exploration, communication, teaching and more.

Read Full Article

Article: Libraries and American Chemical Society Sign Innovative ‘Read and Publish’ Open Access Agreement

Access, Document, Open Decision-Support, Research

Libraries and American Chemical Society Sign Innovative ‘Read and Publish’ Open Access Agreement

Syracuse University Libraries and the Publications Division of the American Chemical Society (ACS) recently signed an innovative “read and publish” open access agreement that will expand the reach of Syracuse University researchers’ scientific contributions.

Open access provides students, faculty and researchers with scholarly work that is published, online, free of charge and free of most copyright and licensing restrictions for further use. Under this transformative “read and publish” agreement, Syracuse University has negotiated with ACS to publish University-affiliated researchers’ scholarly work as open access.

Read Full Article

Article: Building on a year of open data: progress and promise

Access, Open Decision-Support, Research

Building on a year of open data: progress and promise

One year ago, Microsoft launched an Open Data Campaign to help close the data divide between those countries and companies that have the data they need to innovate and those that do not. We learned quickly that this continued divide risks leaving some people behind, without the ability to put data to work and without the ability to generate economic wealth and opportunity more broadly.

To address the challenges of tomorrow, we need to make it easier to open, share and collaborate around data today. That’s why we’re sharing 10 key lessons from the first year of our campaign to help other organizations of all sizes unlock the power of data.

Read Full Article

Article: Participatory Geomatics Network for Coastal Mapping and Monitoring

Access, Geospatial, Open Data, Open Decision-Support

Participatory Geomatics Network for Coastal Mapping and Monitoring

Capacity-building and empowerment using low-cost geomatics equipment, easy-to-use field protocols and semi-automated processing algorithms provide a resilience pathway for coastal communities facing the effects of climate change.

This article presents a participative geomatics project with the goal of increasing southern Québec’s coastal communities’ ability to map and monitor changes in their coastal environment. This co-constructed project aims to develop a participatory network of individuals and groups capable of acquiring, processing and interpreting coastal geospatial data of the Estuary and Gulf of St Lawrence (eastern Canada).

Read Full Article

Article: Rapid7 Acquires Open-Source Community Project Velociraptor

Access, Innovation, Open Decision-Support, Open Space

Rapid7 Acquires Open-Source Community Project Velociraptor

Rapid7 is acquiring Velociraptor, an open-source, endpoint-monitoring, digital forensics and incident response organization and professional community that it will continue to operate as a stand-alone entity while Rapid7 adopts some of its technology. The security analytics and automation company reported the deal on Wednesday and said it will use Velociraptor’s technology to enhance its incident response capabilities. At the same time, it will continue to help support and build the Velociraptor open-source community, Rapid7 says.

“We strongly believe that partnership with the open-source community is one of the most important ways to move the security industry forward and make the digital world a safer place for everyone,” says Richard Perkett, senior vice president of detection and response at Rapid7.

Read Full Article