UK Research and Development Roadmap – GOV.UK

“Research has rapidly improved our understanding of COVID-19. Supported by rapid action by funding bodies, scientists around the world have directed their efforts to this global priority, working collaboratively across countries and disciplines, and sharing findings openly and quickly. Rapid targeted funding has enabled researchers and policy makers to join up to clarify and tackle pressing questions and has enabled businesses to collaborate in new ways to address national needs. For example, the COVID-19 Genomics UK consortium has achieved rapid sequencing of over 50% of all the SARS-CoV-2 genomes in the world. The UK has led the world’s largest randomised control trial for COVID-19, with findings helping the sickest patients not only in the UK but all around the world. We should aspire to this level of openness, connectivity and pace across our whole R&D system….

Crucially, we must embrace the potential of open research practices. First, we will require that research outputs funded by the UK government are freely available to the taxpayer who funds research. Such open publication will also ensure that UK research is cited and built on all over the world. We will mandate open publication and strongly incentivise open data sharing where appropriate, so that reproducibility is enabled, and knowledge is shared and spread collaboratively. Second, we will ensure that more modern research outputs are recognised and rewarded. For example, we will ensure that digital software and datasets are properly recognised as research outputs, so that we can minimise efforts spent translating digital outputs into more traditional formats. Third, we will consider the case for new infrastructure to enable more effective sharing of knowledge between researchers and with industry to accelerate open innovation where possible….”

Welcome — The Turing Way

“The Turing Way is an open source community-driven guide to reproducible, ethical, inclusive and collaborative data science.

Our goal is to provide all the information that data scientists in academia, industry, government and in the third sector need at the start of their projects to ensure that they are easy to reproduce and reuse at the end.

The book started as a guide for reproducibility, covering version control, testing, and continuous integration. But technical skills are just one aspect of making data science research “open for all”.

In February 2020, The Turing Way expanded to a series of books covering reproducible research, project design, communication, collaboration, and ethical research.”

A Community Handbook for Open Data Science

“The Turing Way started in December 2018 and has quickly evolved into a collaborative, inclusive and international endeavor with the aim of uncovering gold standards to ensure reproducible, ethical, inclusive and collaborative data science. How did this happen? I think two ingredients were central to The Turing Way‘s success: extraordinary community building and a clear enticing vision….

Anyone can contribute is a central theme. And not only that: anyone can bring ideas to the table. And folks are doing just that. At the time of writing this post 168 people have contributed. So on average the project has gained 9 new contributors every month since it’s initiation….”

Privacy challenges and research opportunities for genomic data sharing | Nature Genetics

Abstract:  The sharing of genomic data holds great promise in advancing precision medicine and providing personalized treatments and other types of interventions. However, these opportunities come with privacy concerns, and data misuse could potentially lead to privacy infringement for individuals and their blood relatives. With the rapid growth and increased availability of genomic datasets, understanding the current genome privacy landscape and identifying the challenges in developing effective privacy-protecting solutions are imperative. In this work, we provide an overview of major privacy threats identified by the research community and examine the privacy challenges in the context of emerging direct-to-consumer genetic-testing applications. We additionally present general privacy-protection techniques for genomic data sharing and their potential applications in direct-to-consumer genomic testing and forensic analyses. Finally, we discuss limitations in current privacy-protection methods, highlight possible mitigation strategies and suggest future research opportunities for advancing genomic data sharing.

 

Covid-19 Shows Scientific Journals Like Elsevier Need to Open Up – Bloomberg

“One big change brought on by Covid-19 is that virtually all the scientific research being produced about it is free to read. Anyone can access the many preliminary findings that scholars are posting on “preprint servers.” Data are shared openly via a multitude of different channels. Scientific journals that normally keep their articles behind formidable paywalls have been making an exception for new research about the virus, as well as much (if not all) older work relevant to it.

This response to a global pandemic is heartening and may well speed that pandemic to its end. But after that, what happens with scientific communication? Will everything go back behind the journal paywalls?

 

 

Well, no. Open-access advocates in academia have been pushing for decades to make more of their work publicly available and paywall-free, and in recent years they’ve been joined by the government agencies and large foundations that fund much scientific research. Covid-19 has accelerated this shift. I’m pretty sure there’s no going back. …”

Addgene’s AAV Data Hub | Open Neuroscience

“AAV are versatile tools used by neuroscientists for expression and manipulation of neurons. Many scientists have benefited from the high-quality, ready-to-use AAV prep service from Addgene, a nonprofit plasmid repository. However, it can be challenging to determine which AAV tool and techniques are best to use for an experiment. Scientists also may have questions about how much virus to inject or which serotype or promoter should be used to target the desired neuron or brain region. To help scientists answer these questions, Addgene launched an open platform called the AAV Data Hub (https://datahub.addgene.org/aav/) which allows researchers to easily share practical experimental details with the scientific community (AAV used, in vivo model used, injection site, injection volumes, etc.). The goal of this platform is to help scientists find the best AAV tool for their experiments by reviewing combined data from a broad range of research labs. The AAV Data Hub launched in late 2019 and over 100 experiments have since been contributed to this project. The dataset includes details and images from experiments conducted in six different species and several different expression sites….”

Biologer: an open platform for collecting biodiversity data

Abstract:  Background

We have developed a new platform named “Biologer” intended for recording species observations in the field (but also from literature resources and collections). The platform is created as user-friendly, open source, multilingual software that is compatible with Darwin Core standard and accompanied by a simple Android application. It is made from the user’s perspective, allowing everyone to choose how they share the data. Project team members are delegated by involved organisations. The team is responsible for development of the platform, while local Biologer communities are engaged in data collection and verification.

New information

Biologer has been online and available for use in Serbia since 2018 and was soon adopted in Croatia and Bosnia and Herzegovina. In total, we have assembled 536 users, who have collected 163,843 species observation records data from the field and digitalised 33,458 literature records. The number of active users and their records is growing daily. Out of the total number of gathered data, 89% has been made open access by the users, 10% is accessible on the scale of 10×10 km and only 1% is closed. In the future, we plan to provide a taxonomic data portal that could be used by local and national initiatives in Eastern Europe, aggregate all data into a single web location, create detailed data overview and enable fluent communication between users.

Biologer: an open platform for collecting biodiversity data

Abstract:  Background

We have developed a new platform named “Biologer” intended for recording species observations in the field (but also from literature resources and collections). The platform is created as user-friendly, open source, multilingual software that is compatible with Darwin Core standard and accompanied by a simple Android application. It is made from the user’s perspective, allowing everyone to choose how they share the data. Project team members are delegated by involved organisations. The team is responsible for development of the platform, while local Biologer communities are engaged in data collection and verification.

New information

Biologer has been online and available for use in Serbia since 2018 and was soon adopted in Croatia and Bosnia and Herzegovina. In total, we have assembled 536 users, who have collected 163,843 species observation records data from the field and digitalised 33,458 literature records. The number of active users and their records is growing daily. Out of the total number of gathered data, 89% has been made open access by the users, 10% is accessible on the scale of 10×10 km and only 1% is closed. In the future, we plan to provide a taxonomic data portal that could be used by local and national initiatives in Eastern Europe, aggregate all data into a single web location, create detailed data overview and enable fluent communication between users.

Universal Funders’ Policy on Open Deposition of Publication-Associated Records

“A condition of being awarded funding by [FUNDER] is that researchers commit to making all source evidence such as data and computer code supporting published research — hence referred to in this policy as the records — publicly available as Open Access outputs, to the maximum extent permitted by relevant legal and ethical requirements. Where the materials can be legally and ethically published and made available, they must be released in synchrony with peer-reviewed outputs rather than at the end of the project. “Data will be available upon (reasonable) request from the corresponding author(s)” will no longer be acceptable in publications featuring work funded by [FUNDER]. …”