A versatile and customizable low-cost 3D-printed open standard for microscopic imaging | Nature Communications

Abstract:  Modern microscopes used for biological imaging often present themselves as black boxes whose precise operating principle remains unknown, and whose optical resolution and price seem to be in inverse proportion to each other. With UC2 (You. See. Too.) we present a low-cost, 3D-printed, open-source, modular microscopy toolbox and demonstrate its versatility by realizing a complete microscope development cycle from concept to experimental phase. The self-contained incubator-enclosed brightfield microscope monitors monocyte to macrophage cell differentiation for seven days at cellular resolution level (e.g. 2??m). Furthermore, by including very few additional components, the geometry is transferred into a 400 Euro light sheet fluorescence microscope for volumetric observations of a transgenic Zebrafish expressing green fluorescent protein (GFP). With this, we aim to establish an open standard in optics to facilitate interfacing with various complementary platforms. By making the content and comprehensive documentation publicly available, the systems presented here lend themselves to easy and straightforward replications, modifications, and extensions.

10M ORCID iDs! | ORCID

“At the end of 2012, just three months after we launched the ORCID registry, we were thrilled to be able to share that nearly 50,000 researchers had already registered for an iD. Ten months after that, we celebrated the ORCID record growing to nearly 250,000 (with 80 Members!) All told, it took us just a little over two years to grow to 1,000,000 iDs, and nine months after that, in 2015, we hit 1.5 million iDs. 

Since 2015 we’ve been steadily growing and exceeding even our own high expectations:

In 2015, the record grew by 788,650 records,
In 2016, by 1,068,295,
In 2017, 1,388,796,
In 2018, it grew by 1,585,851,
In 2019, by 2,006,672, and
In 2020 (so far), it’s grown by 2,293,631! 

And just last week ORCID hit another major milestone: 10 million registered ORCID iDs! …”

NISO Voting Members Approve Work to Update Journal Article Versions (JAV)

“The National Information Standards Organization (NISO) announced today that their Voting Members have approved a new work item to update the 2008 Recommended Practice, NISO RP-8-2008, Journal Article Versions (JAV): Recommendations of the NISO/ALPSP JAV Technical Working Group. A NISO Working Group is being set up, and work is expected to begin in early 2021. 

Publication practices have changed rapidly since the publication of the original recommendations. For example, preprints have become much more important as a publication type in many disciplines, and publishers are increasingly experimenting with new ways to publish, update, and keep research alive. All of these versions of an article are important and citable, making the concept of a single ‘version of record’ less relevant. These additional processes to support public availability make the consistent assignment of DOIs to one or more versions challenging. 

The NISO JAV working group will define a set of terms for each of the different versions of content that are published, as well as a recommendation for whether separate DOIs should be assigned to them. They will address questions such as: Should there be a single DOI for an article, regardless of version? Different DOIs for each version? How are the identifiers connected and used? How do we define a version? As with all NISO output, the group’s draft recommendations will be shared for public comment before publication….”

Standards Committee Votes – 11/8/2020 – Association for Information Science and Technology | ASIS&T

“1) Voted YES on Approval of Proposed New Work Item: Update NISO RP-8-2008, Journal Article Versions (JAV)

 

Question:

Do you approve of a Proposed New Work Item: Update NISO RP-8-2008, Journal Article Versions (JAV)?

Description:

This ballot is to approve a proposed new work item to Update NISO RP-8-2008, Journal Article Versions (JAV) [https://www.niso.org/publications/niso-rp-8-2008-jav] to take into account publication practices that have been adopted over the past 12 years, especially the increasing circulation of preprints and the application of DOIs across the landscape….”

New SPARC Europe report out: Scoping the Open Science Infrastructure Landscape in Europe – SPARC Europe

“Service providers could benefit from:

 

Sharing lessons learnt. This might involve developing communities of practice and guidance; pooling resources and working with initiatives such as Invest in Open Infrastructure (IOI) and JROST. 
Following good governance practices. This allows the community to trust that the infrastructure or service will be steered by the needs of the community and stay true to the values of research.
Going open source and adopting open standards.  “Despite a strong uptake of open source and open standards by many, challenges remain for some in sharing good governance, open content and applying open standards,” wrote the authors.
Diversifying fund-raising efforts, upskilling to embrace a range of business revenue models. This allows the organisation to spread financial risk….”

CHORUS and DataCite sign MOU to advance linking and discoverability – CHORUS

“CHORUS and DataCite have signed a two-year Memorandum of Understanding (MOU) to coordinate efforts to adopt identifiers and standards to manage access to and reporting of research outputs.

Authoritative connections between researchers and their works, funding sources, and affiliations, are essential for delivering public access to scholarly content. As not-for-profit organizations engaged in supporting discoverability in scholarly communications, both DataCite and CHORUS have an important contribution to make creating and supporting these links.

The organizations commit to dialog and cooperation on the following topics:

Supporting simple and non-ambiguous links between datasets, researchers and their funding
Displaying links between CHORUS content and DataCite DOIs in the CHORUS dashboards and reports
Building awareness of DataCite services among funding agency researchers and administrators
Encouraging the use of persistent identifiers for researchers and organizations to support public access to research works …”

There’s A PID For That! Next Steps in Establishing a National PID Strategy – Jisc scholarly communications

“A stakeholder group was therefore formed earlier this year, with representatives from all disciplines and sectors — funders, HEIs, infrastructure providers, libraries, publishers, researchers, research managers, and more. At an initial meeting of this group in April, participants discussed the five persistent identifiers (PIDs) that have been deemed high priority for improving access to UK research. These are ORCID iDs for people, Crossref and DataCite DOIs for outputs, Crossref grant DOIs, ROR identifiers for organisations, and RAiDs for projects.  This was followed by five focus group meetings during May and June, each focused on one of the priority PIDs….”

The Data Nutrition Project

“A “nutrition label” for datasets.

The Data Nutrition Project aims to create a standard label for interrogating datasets for measures that will ultimately drive the creation of better, more inclusive algorithms.

Our current prototype includes a highly-generalizable interactive data diagnostic label that allows for exploring any number of domain-specific aspects in datasets. Similar to a nutrition label on food, our Dataset Nutrition Label aims to highlight the key ingredients in a dataset such as meta-data and populations, as well as unique or anomalous features regarding distributions, missing data, and comparisons to other ‘ground truth’ datasets. We are currently testing our label on several datasets, with an eye towards open sourcing this effort and gathering community feedback.

The design utilizes a ‘modular’ framework that can be leveraged to add or remove areas of investigation based on the domain of the dataset. For example, Dataset Nutrition Labels for data about people may include modules about the representation of race and gender, while Nutrition Labels for data about trees may not require that module.

To learn more, check out our live prototype built on the Dollars for Docs dataset from ProPublica. A first draft of our paper can be found here….”

Blog – Europe PMC: Announcing the new version of SciLite – the Europe PMC tool for highlighting annotations

“This month, Europe PMC released a new version of SciLite, a powerful tool for highlighting annotations in life sciences publications. SciLite is powered by the Europe PMC annotation platform via the open annotation API, which provides access to over 1.3 billion annotations. Highlighting annotations in the text enables users to easily scan the article and locate key biological entities, such as genes/proteins, accession numbers, protein interactions, diseases, gene-disease relationship and more….”

4Science, share your knowledge: research data and digital libraries

“Our mission is to support universities, research and cultural institutes in managing the different phases of a digital project.

To successfully fulfill this mission 4Science chose DSpace, the most widely used repository software in the world.

As a DSpace Registered Service Provider and thanks to our Team of experts, that includes 2 DSpace Committers, we provide any kind of support to your repository.

4Science is constantly working with the DSpace Community on improving the platform, developing new functionalities and add-on modules and implementing compliancy with international standards.

Thanks to our natural inclination towards innovation and our deep understanding of the Research Data & Information and the Cultural Heritage domains, we developed two out-of-the-box configurations of DSpace that meet the requirements of these two areas….”

Sharing and organizing research products as R packages | SpringerLink

Abstract:  A consensus on the importance of open data and reproducible code is emerging. How should data and code be shared to maximize the key desiderata of reproducibility, permanence, and accessibility? Research assets should be stored persistently in formats that are not software restrictive, and documented so that others can reproduce and extend the required computations. The sharing method should be easy to adopt by already busy researchers. We suggest the R package standard as a solution for creating, curating, and communicating research assets. The R package standard, with extensions discussed herein, provides a format for assets and metadata that satisfies the above desiderata, facilitates reproducibility, open access, and sharing of materials through online platforms like GitHub and Open Science Framework. We discuss a stack of R resources that help users create reproducible collections of research assets, from experiments to manuscripts, in the RStudio interface. We created an R package, vertical, to help researchers incorporate these tools into their workflows, and discuss its functionality at length in an online supplement. Together, these tools may increase the reproducibility and openness of psychological science.

 

Being Fair about the Design of FAIR Data Standards | Zenodo

Abstract:  Since 2014 the FAIR data movement has been rapidly altering the landscape of data sharing and re-use. Support for the FAIR movement has seen the evolution of disciplinary-specific standards to foster data that are “finable, accessible, interoperable and reusable.” While these exciting developments should not be minimised, it is important to interrogate how these standards are set. Key questions to ask include how representation in standard setting communities is addressed; what infrastructures and resources these emergent standards are reliant on; and how standards dictate specific interpretations of “value” and “valuable data.” Asking such questions introduces a needed reflexivity into FAIR discussions, as standard setters interrogate what data practices commit present—and future—researchers to.

Celebrating the Five Year Anniversary of the UK ORCID Consortium – Jisc scholarly communications

“August 2020 sees the 5-year anniversary of the UK ORCID consortium. The evolution of ORCID and the UK Consortium can be viewed as a change programme. If we look back and reflect, what have been the drivers for change and what improvements can we celebrate?…

The range and complexity of outputs that ORCID identifiers are associated with has expanded as well, as new systems and ways of capturing information emerge – especially as we move to a data rich, information-centric open science model of scholarship. As such, the power of interconnected PIDs with the personal identifier of ORCID ID embedded, gives deeply intertwined and more useful information. These potential benefits can be realised as the various systems and identifiers mature and adoption improves. Examples of associations with unique persistent person identities are: works (e.g. works identified with a DOI); organisations (identified, for example with a ROR id); affiliations and workflows which can be examined via the events captured in PID Graphs. A project identifier such as RAiD allows you to associate people, data, works and funding with a long term effort, track the impact of efforts over the long term, and focus on the narrative, rather than a particular researcher or funding stream. This evolving landscape of interconnection allows us to build better, more effective scholarly machines, to do open research on a better, more cohesive and collaborative scale….”

Data Sharing in a Time of Pandemic: Patterns

“The resulting recommendations and guidelines on data sharing,

1

 published in final form on Jun 30, 2020, are a thorough and comprehensive overview of how to share data (and research software) from multiple disciplines to inform response to a pandemic, along with guidelines and recommendations on data sharing under the present COVID-19 circumstances. It is a long document (more than 140 pages) but is very thorough and well structured….”

FAIRsFAIR

“FAIRsFAIR – Fostering Fair Data Practices in Europe – aims to supply practical solutions for the use of the FAIR data principles throughout the research data life cycle. Emphasis is on fostering FAIR data culture and the uptake of good practices in making data FAIR. FAIRsFAIR will play a key role in the development of global standards for FAIR certification of repositories and the data within them contributing to those policies and practices that will turn the EOSC programme into a functioning infrastructure.

In the end, FAIRsFAIR will provide a platform for using and implementing the FAIR principles in the day to day work of European research data providers and repositories. FAIRsFAIR will also deliver essential FAIR dimensions of the Rules of Participation (RoP) and regulatory compliance for participation in the EOSC. The EOSC governance structure will use these FAIR aligned RoPs to establish whether components of the infrastructure function in a FAIR manner….”