? sci2sci – “GitHub for scientists” – AI-friendly research data management and publishing platform | Grants | Gitcoin

“At sci2sci, we are building an electronic lab notebook and a publishing platform in one interface. This will allow to store all experimental data and metadata in one place, and quickly release it in public access with one click. 

In a nutshell, we offer full stack data publishing – from the experiment planning through raw data acquisition and analysis to the final research report – all in a single platform, with a number of benefits that cannot be offered by a current journal pdf manuscript:…”

XCIST – an open access x-ray/CT simulation toolkit – IOPscience

Abstract:  Objective: X-ray-based imaging modalities including mammography and computed tomography (CT) are widely used in cancer screening, diagnosis, staging, treatment planning, and therapy response monitoring. Over the past few decades, improvements to these modalities have resulted in substantially improved efficacy and efficiency, and substantially reduced radiation dose and cost. However, such improvements have evolved more slowly than would be ideal because lengthy preclinical and clinical evaluation is required. In many cases, new ideas cannot be evaluated due to the high cost of fabricating and testing prototypes. Wider availability of computer simulation tools could accelerate development of new imaging technologies. This paper introduces the development of a new open-access simulation environment for X-ray-based imaging. Approach: The X-ray-based Cancer Imaging Simulation Toolkit (XCIST) is developed in the context of cancer imaging, but can more broadly be applied. XCIST is physics-based, written in Python and C/C++, and currently consists of three major subsets: digital phantoms, the simulator itself (CatSim), and image reconstruction algorithms; planned future features include a fast dose-estimation tool and rigorous validation. To enable broad usage and to model and evaluate new technologies, XCIST is easily extendable by other researchers. To demonstrate XCIST’s ability to produce realistic images and to show the benefits of using XCIST for insight into the impact of separate physics effects on image quality, we present exemplary simulations by varying contributing factors such as noise and sampling. Main Results: The capabilities and flexibility of XCIST are demonstrated, showing easy applicability to specific simulation problems. Geometric and X-ray attenuation accuracy are shown, as well as XCIST’s ability to model multiple scanner and protocol parameters, and to attribute fundamental image quality characteristics to specific parameters. Significance: This work represents an important first step toward the goal of creating an open-access platform for simulating existing and emerging X-ray-based imaging systems.

LSHTM Press launches with a mission of equity in publishing in global health | LSHTM

“A new publishing platform for open access biomedical research has launched. LSHTM Press will provide an open access platform to publish peer-reviewed research and high-quality educational resources, in accordance with the LSHTM mission to improve health and health equity in the UK and worldwide.

The Press is a new initiative, developed in response to the increasing costs of publishing open access, and the many mandates and policies from funders and governments around the world. It will facilitate innovative and experimental publishing methods while striving towards equity in academic publishing in global health.

It launches with and will continue to develop a focus on equity, diversity and inclusion (EDI), and is in alignment with central LSHTM vision and values. Two dedicated EDI leads sit on the LSHTM Press Steering Committee, and the whole team is committed to promoting inclusivity and reducing barriers….”

Scholia for Software

Abstract:  Scholia for Software is a project to add software profiling features to Scholia, which is a scholarly profiling service from the Wikimedia ecosystem and integrated with Wikipedia and Wikidata. This document is an adaptation of the funded grant proposal. We are sharing it for several reasons, including research transparency, our wish to encourage the sharing of research proposals for reuse and remixing in general, to assist others specifically in making proposals that would complement our activities, and because sharing this proposal helps us to tell the story of the project to community stakeholders.

A “scholarly profiling service” is a tool which assists the user in accessing data on some aspect of scholarship, usually in relation to research. Typical features of such services include returning the biography of academic publications for any given researcher, or providing a list of publications by topic. Scholia already exists as a Wikimedia platform tool built upon Wikidata and capable of serving these functions. This project will additionally add software-related data to Wikidata, develop Scholia’s own code, and address some ethical issues in diversity and representation around these activities. The end result will be that Scholia will have the ability to report what software a given researcher has described using in their publications, what software is most used among authors publishing on a given topic or in a given journal, what papers describe projects which use some given software, and what software is most often co-used in projects which use a given software.



Communities, Commoning, Open Access and the Humanities: An Interview with Martin Eve – ScienceOpen

Abstract:  Leading open access publishing advocate and pioneer Professor Martin Paul Eve considers several topics in an interview with WPCC special issue editor Andrew Lockett. These include the merits of considering publishing in the context of commons theory and communing, digital platforms as creative and homogenous spaces, cosmolocalism, the work of intermediaries or boundary organisations and the differing needs of library communities. Eve is also asked to reflect on research culture, the academic prestige economy, the challenges facing the humanities, digital models in trade literature markets and current influences in terms of work in scholarly communications and recent academic literature. Central concerns that arise in the discussion are the importance of values and value for money in an environment shaped by increasing demands for policies determined by crude data monitoring that are less than fully thought through in terms of their impact and their implications for academics and their careers.


R Discovery partners with Springer Nature to create an open-access content bank for global researchers – CACTUS

“R Discovery, a Cactus Communications (CACTUS) brand, has partnered with Springer Nature, global academic publisher, to help broaden the reach of open access (OA) content to the global researcher community. The inclusion of Springer Nature’s OA portfolio into R Discovery means that the platform offers its over 1.4 million researchers access to high-quality OA content in over 32,000 journals worldwide across a breadth of subject areas….”

Five industry leaders on the future of publishing platforms | Research Information

“Penev, Pensoft: It must be a difficult exercise for publishing platforms and their developers to switch from technologies initially designed for subscription journals. Luckily for us at ARPHA, we don’t have to face this challenge, as it has been designed as a fully open-access platform from the very start. Instead, we are simply continuing our work towards the much anticipated evolution from open access to open science. 

One way for platforms to embrace open science – apart from prompting free and easy access to research publications from day one – is opening up ‘non-conventional’ research work, including early research and small, yet integral bits and pieces that comprise scientific breakthroughs. Favourite examples are grant proposals, datasets, data management plans, workshop reports, software descriptions, conference abstracts and posters. 

Bailey, 67 Bricks: We’ve seen some recognition of the fact that publishers’ primary customers are shifting, from libraries, consortia and institutions to researchers, thanks to the open-access movement. Publishers whose customer data is in great shape and can therefore respond quickly to changing needs and trends will be at an advantage in this new market, since customers at an individual level are much less likely to suffer from inertia than B2B subscription contracts. This B2B to B2C movement is still nascent and requires a new mindset from both publishers and platforms.

In terms of the platforms themselves, open and digital-first platforms, such as F1000 and PLOS, have taken steps including facilitating preprint deposits, promoting open peer review and requiring open data – all of which challenge some of the traditional publishing processes and take advantage of the available technology. 

Eckert, Frontiers: I believe platforms, which were developed with the sole aim to enable open access, provide the most powerful solutions for our move towards open science as they do not suffer from compromises in workflows or being adopted as an afterthought in the publishing process. Open-science platforms benefit from fully leveraging the widespread dissemination of research advances without barriers to access and therefore drive visibility and impact for scientists. The myth that open science is of lower quality has also set the standards high for open-science platforms to perform better than legacy solutions in quality control, assurance and efficiency, while allowing for an expansion of innovation and promoting collaboration.

Bazargan, RVT: Open access has simplified and streamlined the requirements of publishing platforms, in that no subscription or authentication of the reader is needed. On the other hand, the submission systems have more to do, mainly to work out article processing charges (APCs) using complex formulae. In addition, the submission system, directly or indirectly, needs to collect the funds from the author. The proliferation of Plan S transition models have added further complications to APC calculation and management.

The move to open science has meant that data relating to publications needs to be openly available and in as widely readable formats as possible. This requires publishing platforms to partner with third parties that specialise in hosting different types of data. Ideally, the data should be viewable directly via the platforms and should be linked closely with the relevant section of the publication.

Hargitt, Literatum: Open access has opened the industry’s eyes to new business models that rely on enriched content offerings. Publishers are considering branching into new content types so they can better identify, develop and monetise their audiences and high-value content spaces. Open science has also sparked a conversation about embracing technologies that enable publishers to take new strides. Research that incorporates media and data assets requires new services to be integrated, or natively supported on platforms, requiring an overall modernisation of supporting content management systems….”

Guide to Plan S compliance in OJS

“For cOAlition S funded research covered by Plan S requirements, all peer-reviewed scholarly articles must be published in venues that fulfil the “Requirements for Publication Venues.” Individual publication venues (such as journals publishing on OJS) are responsible for ensuring that they meet these requirements. Journals that do not meet these requirements will not be suitable for scholarly articles resulting from cOAlition S-funded research.

Many of the Plan S requirements for publication venues represent best practices for quality, discoverability, and interoperability in scholarly publishing. We recommend that journals adopt these practices regardless of whether they intend to publish scholarly articles resulting from Coalition S-funded research….

This guide is intended for journals published on OJS which intend to meet the Requirements for Publication Venues articulated by Plan S under Part III: Technical Guidance and Requirements. This guide is modelled around the Plan S requirements, with sections of this guide mirroring the sections (1.1 and 1.2) of the Plan S requirements. The guide provides specific recommendations for implementing the requirements in OJS. Where suitable we have linked to other PKP documentation and guidance which provides additional details on the implementation of specific features and specifications.

While we will do our best to keep this guide up-to-date, the Plan S documentation should be relied upon for the most current and detailed information….”

$10M to support open-access and open-source research | UdeMNouvelles

“By awarding a $10-million grant to Coalition Publica through the Major Science Initiatives Fund 2023-2029, the Canada Foundation for Innovation is helping to address the ongoing need to operate and maintain research facilities of national importance, enabling Canadian researchers to undertake activities that rival those of their international colleagues.

Coalition Publica is developing an open, non-commercial infrastructure for digital research, dissemination and scholarly publication in the humanities and social sciences. The infrastructure is based on the complementarity of two leading technology solutions dedicated to open access and open science.

The first of those solutions is the erudit.org dissemination platform of the Érudit Consortium of Université de Montréal (UdeM), Université Laval and Université du à Montréal, while the second is the Open Journal Systems editing and publishing software developed by the Public Knowledge Project at Simon Fraser University….”

Canada Foundation for Innovation renews its support for Coalition Publica | 19 August 2022

“Coalition Publica will strengthen its digital services to the Canadian and international scholarly community with continued investment from CFI. The Canada Foundation for Innovation (CFI) is awarding a $10 million grant to Coalition Publica under the Major Science Initiatives Fund 2023-2029. Through this program, CFI contributes to the ongoing operation and maintenance needs of research facilities of national importance in order to enable Canadian researchers to undertake world-class research. Coalition Publica is developing an open, non-commercial infrastructure for digital research, dissemination, and scholarly publishing. It is based on the complementarity between the publishing software Open Journal Systems, developed by the Public Knowledge Project (Simon Fraser University (SFU)), and the erudit.org dissemination platform of the Érudit Consortium (Université de Montréal, Université Laval, Université du Québec à Montréal), two leading technological solutions dedicated to open access and open science. In collaboration with the editorial teams of more than 250 scholarly and cultural journals, Coalition Publica also offers access to the largest corpus of Canadian research results in the humanities and social sciences. More than 220,000 publications are available, and 8,000 new articles are disseminated each year. Rich and diverse, the collections are representative of Canadian and international research and creation: archaeology, economics, history, literary studies, psychology, education… They are consulted each year by nearly 6 million users worldwide….”

NSF Grant for New STEM-focused Commons | Platypus – the Humanities Commons Blog

by Kathleen Fitzpatrick

The Commons team is delighted to have been awarded one of the inaugural FAIROS RCN grants from the NSF, in order to establish DBER+ Commons. That’s a big pile of acronyms, so here’s a breakdown: the NSF is of course the National Science Foundation, one of the most important federal funding bodies in the United States, and a new funder for us. The FAIROS RCN grant program was launched this year by the NSF in order to invest in Findable, Accessible, Interoperable, Reusable Open Science (FAIROS) by supporting the formation and development of Research Coordination Networks (RCN) dedicated to those principles.

We have teamed up with a group of amazing folks at Michigan State University who are working across science, technology, engineering, math, and more traditional NSF fields, all of whom are focused on discipline-based education research (DBER) as well as other engaged education research methodologies (the +). Our goal for this project is to bring them together with their national and international collaborators in STEM education to create DBER+ Commons, which will use — and crucially, expand — the affordances of the HCommons network and promote FAIR and CARE (Collective Benefit, Authority to control, Responsibility, Ethics) practices, principles, and guidelines in undergraduate, postbaccalaureate, graduate, and postdoctoral science education research activities.


FOLIO + ReShare | August 2022

“CAVAL is the first in Australia to be implementing FOLIO (supported by IndexData) as we see this modern, open-source Library Management Platform benefiting and empowering the entire library community. In the next phase we are also looking at offering a new vendor-neutral resource-sharing platform, ReShare, to our members and the wider community….”

more info: https://librarytechnology.org/pr/27641

Oxford University Press unlocks significant next step in digital-first publisher journey – FE News

“University Press (OUP) has today announced the migration of its books content to Oxford Academic—the online platform for its academic research.

The expansion of the platform to include books, as well as journals, will further the reach of academic resources from OUP and society partners. As it stands, more than 42,000 books and over 500,000 chapters have so far been uploaded to Oxford Academic, joining the 500 journals and approximately 3 million journal articles already hosted on the platform.

By collating core research books and journals onto one online platform, OUP is better enabling its users to rapidly share and seamlessly connect ideas that advance research. This will continue a cycle of scholarship that furthers the Press’s mission to create world-class academic and educational resources and make them available as widely as possible. The platform will be further expanded and updated over time to provide the most effective and accessible service for users and customers….”

A Possible Fix For Scientific (and Academic) Publishing | Peer Review – News and Blog

“This is a proposal for a software platform that may help the academic community solve these problems, and more….

Peer Review [the proposed platform] allows scholars, scientists, academics, and researchers to self organize their own peer review and refereeing, without needing journal editors to manually mediate it. The platform allows review and refereeing to be crowdsourced, using a reputation system tied to academic fields to determine who should be able to offer review and to referee.

The platform splits pre-publish peer review from post-publish refereeing. Pre-publish review then becomes completely about helping authors polish their work and decide if their articles are ready to publish. Refereeing happens post-publish, and in a way which is easily understandable to the lay reader, helping the general public sort solid studies from shakey ones.


Peer Review is being developed open source. The hope is to form a non-profit to develop it which would be governed by the community of academics who use the platform in collaboration with the team of software professionals who build it (a multi-stakeholder cooperative)….”