Harvard researchers to help develop cloud-based NIH Data Commons platform – Harvard Gazette

“The National Institute of Health has announced that Harvard co-Principal Investigators Dr. Mercè Crosas and Dr. Timothy Clark are NIH Data Commons Pilot Phase Awardees….

The awards are part of the National Institutes of Health’s new Data Commons program, which will be implemented in a 4-year pilot phase to explore the feasibility and best practices for making digital objects including very large-scale genomics resources, available and computable through collaborative platforms. This will be done on public clouds, virtual spaces where service providers make resources, such as applications and storage, available over the internet. The goal of the NIH Data Commons Pilot Phase is to accelerate biomedical discoveries by making biomedical research data Findable, Accessible, Interoperable, and Reusable (FAIR) for more researchers….”

Rebus Launches an Open Reading Initiative | REBUS Foundation

“After conducting primary research into the viability of a web-based system for open reading, we are now moving forward with its development, thanks to generous funding from The Andrew W. Mellon Foundation. The Mellon Foundation is a leader in support to the arts and humanities, directed at the long-term well-being of diverse and democratic societies.

The US$873,000, two-year grant funds our ongoing work in the conception, design, and development of a reading and research platform, based on open principles and optimizing the reader’s experience. Users will be able to read, take notes, cite, and organize their collection, helping them write or produce other outputs that best suit their needs. A big focus is on developing partnerships with libraries and university presses as we develop the software, so that our work reflects the needs of the whole ecosystem….

Established in April 2016, the Rebus Foundation is a Canadian non-profit organization. Our objective is to help create an alternative publishing ecosystem, based on open principles. This reading initiative adds an important complement to the open publishing and project management platform of Rebus Community and the Rebus Press….”

Announcing Fulcrum Integration Plans – Editoria

“The Editoria Community is very pleased to welcome Michigan Publishing into our circle of forward-thinking publishers architecting the future of books production workflow together.

Michigan Publishing, a division of the University of Michigan Library, is the hub of scholarly publishing for the University of Michigan Press and Maize imprints. Michigan Publishing also develops Fulcrum, the community-based, open source platform which supports publishers like Lever Press and aggregations such as the ACLS Humanities Ebook Collection.

“Together, Editoria and Fulcrum provide an open source, end-to-end solution for digital first monograph publishing,” says Charles Watkinson, Associate University Librarian for Michigan Publishing. “This is a revolutionary offering for library-based publishers committed to implementing an academy-owned tool chain.”…”

On the practical implementation of Plan S | Martin Paul Eve | Professor of Literature, Technology and Publishing

“I here set out some of the practical challenges and concrete steps to implementation that I believe could help or hinder each of the points. Of course, this post is somewhat speculative since we have but very few details on Plan S….”


Riffyn launches Open Access for scientists at non-profits | Riffyn

“Riffyn, a global provider of cloud-based experiment design and data analytics software, has launched Riffyn Open Access which provides free use of its patented Scientific Development Environment (SDE) to any member of a non-profit organization. Open Access users have a full-featured Riffyn SDE account to create and openly share reusable experimental methods and data on the platform….”

Evaluation of a novel cloud-based software platform for structured experiment design and linked data analytics | Scientific Data

Abstract:  Open data in science requires precise definition of experimental procedures used in data generation, but traditional practices for sharing protocols and data cannot provide the required data contextualization. Here, we explore implementation, in an academic research setting, of a novel cloud-based software system [Riffyn] designed to address this challenge. The software supports systematic definition of experimental procedures as visual processes, acquisition and analysis of primary data, and linking of data and procedures in machine-computable form. The software was tested on a set of quantitative microbial-physiology experiments. Though time-intensive, definition of experimental procedures in the software enabled much more precise, unambiguous definitions of experiments than conventional protocols. Once defined, processes were easily reusable and composable into more complex experimental flows. Automatic coupling of process definitions to experimental data enables immediate identification of correlations between procedural details, intended and unintended experimental perturbations, and experimental outcomes. Software-based experiment descriptions could ultimately replace terse and ambiguous ‘Materials and Methods’ sections in scientific journals, thus promoting reproducibility and reusability of published studies.

Riffyn Open Access Policy

“Any person affiliated with a non-profit organization, whose mission aligns with Riffyn’s values — notably a commitment to truth, integrity, democratic discourse, diversity of idea and cultures, community, equal opportunity, and social and environmental stewardship — can obtain access to the Riffyn SDE Software-as-a-Service (SaaS) and the publicly-shared content stored therein, via a no-cost Riffyn Open Access Account.  A Riffyn Open Access Account will be granted upon acceptance of Riffyn’s Individual Open Access Account Agreement. The agreement implements the principles outlined in this policy….”

Joint Statement on Open Access for Researchers via Plan S

“Plan S calls for all scientific publications on the results of research funded by national and European research councils and funding bodies to be published in compliant Open Access journals or on compliant Open Access platforms by 01 January 2020. The plan was initiated by the Open Access Envoy of the European Commission and Science Europe and will be implemented by cOAlition S. The coalition currently includes 11 national funders and is supported by the European Commission and European Research Council. Plan S consists of 10 principles to be enacted by coalition members. We, representatives of early-career and senior researchers in Europe, commend cOAlition S for taking this bold and ambitious step towards Open Access and offer our support as well as comments on implementing Plan S….

(4) We agree with immediate Open Access and that there should be no embargo periods on publications. We note a lack of explicit reference to the role of ‘green’ publishing and the relation between green and ‘gold’ publishing in Plan S. We understand that the green route in Plan S refers to self-archiving a final version of a publication without an embargo period whereby the author retains copyright under an open licence. We believe that such a green route is a viable and sustainable alternative to the fee-based gold route and could play a key role in the shift to immediate Open Access. We encourage RPOs and RFOs not to focus solely on the gold route but to adopt an ‘always green optionally gold’ publishing policy. We also encourage publishers to offer a green route option for publications as per criteria in Plan S….”


PKP and SciELO announce development of open source Preprint Server system | SciELO in Perspective

“In recognition of SciELO’s twentieth anniversary, the Public Knowledge Project (PKP) and SciELO Program are entering into an agreement to develop a Preprint Server system on the principles that have guided these two organizations over the last two decades.

These governing principles include recognizing the value of: (a) independent manuscript evaluation systems and related services that are open to the academic community on a global basis, (b) comprehensive workflows for scholarly publishing that include options for preprint and post-publication commentary; and (c) affordable open source software systems for the underlying infrastructure for scholarly communication.

PKP and SciELO plan to collaborate on the building of a Preprint Server system fully interoperable with Open Journal System (OJS) and other publishing systems that will serve SciELO Network journals and that will be made publicly available to other organizations to operate….