GitHub repositories with links to academic papers: Public access, traceability, and evolution – ScienceDirect

Abstract:  Traceability between published scientific breakthroughs and their implementation is essential, especially in the case of open-source scientific software which implements bleeding-edge science in its code. However, aligning the link between GitHub repositories and academic papers can prove difficult, and the current practice of establishing and maintaining such links remains unknown. This paper investigates the role of academic paper references contained in these repositories. We conduct a large-scale study of 20 thousand GitHub repositories that make references to academic papers. We use a mixed-methods approach to identify public access, traceability and evolutionary aspects of the links. Although referencing a paper is not typical, we find that a vast majority of referenced academic papers are public access. These repositories tend to be affiliated with academic communities. More than half of the papers do not link back to any repository. We find that academic papers from top-tier SE venues are not likely to reference a repository, but when they do, they usually link to a GitHub software repository. In a network of arXiv papers and referenced repositories, we find that the most referenced papers are (i) highly-cited in academia and (ii) are referenced by repositories written in different programming languages.


Live Webinar: Open systems and library analytics – 1501970

“Open source software and interoperable services for library management and analytics provide libraries with more choice in how to deploy, support and develop mission-critical applications. Join this webinar to learn more about EBSCO’s support for FOLIO, the open source library services platform, and Panorama, an interoperable application for library analytics.”

The Advanced Research Consortium Joins the Open Library Foundation as Project Member | Open Library Foundation

“The Advanced Research Consortium (ARC) has joined the Open Library Foundation as a Project Member. By joining the Open Library Foundation, ARC is able to leverage the community of projects that are part of the Open Library Foundation.

The Advanced Research Consortium (ARC) serves as a hub of humanities virtual research environments or research nodes. ARC provides support, coordination, and a set of evolving standards for more than 200 digital humanities projects that are open access and peer reviewed by five period-specific and thematic research communities, with more projects and communities joining every year. The ARC Catalog is available through BigDIVA (Big Data Infrastructure Visualization Application), a web-based search and discovery service designed for humanities scholars and students….”

Projects | Open Library Foundation

“Project members are communities that build or support open source software for libraries or within the information science space and call the Foundation their administrative home.

The Foundation supports these projects in a variety of ways and project members have access to professional services that the Foundation provides.”

Getty Publications: how Quire is creating solutions to open access publishing – MuseumNext

“In anticipation of MuseumNext’s Digital Collections Summit next week (4-6 October) we caught up with Erine Cecele Dunigan, Community Manager for Quire, an open-source digital publishing tool developed by Getty.

Erin will be giving a talk on Wednesday 6 October entitled, Open Access: Getty’s Approach to Digital Collection Catalogues….

Quire is a modern digital publishing tool developed by Getty. It’s ideal for creating dynamic publications in a variety of formats, including web, print, and e-book. In addition to being optimised for scholarly and visually rich publishing, Quire books are designed for longevity, sustainability, and discoverability.

Getty originally conceived Quire as a solution to its open access publishing needs, but the tool quickly gained the attention of other organisations within the fields of digital humanities, arts, and academia. While access is currently available for free upon request, we will be launching as a fully open-source publishing tool by Spring 2022. Open-sourcing Quire will enable others to leverage the work Getty has done to create, customise, and distribute critical digital scholarship online, at a low cost, and with little ongoing maintenance….”

PALNI and PALCI Partner to Remove Barriers to Hyku Adoption with IMLS Grant Award

“The Institute of Museum and Library Services (IMLS) has awarded $248,050 to the Private Academic Library Network of Indiana (PALNI) in partnership with The Partnership for Academic Library Collaboration & Innovation (PALCI) for Hyku for Consortia: Removing Barriers to Adoption as part of the National Leadership Grants for Libraries Program. IMLS received 172 applications requesting more than $47 million in funding and selected 39 applicants to receive awards during this grant cycle. With this award, the partners will increase the flexibility, accessibility, and usability of Hyku, the multi-tenant repository platform system.  

Repositories are a critical piece of library infrastructure, enabling access to many types of digital materials created by an institution’s students, faculty, staff, and researchers. Libraries, cultural heritage institutions, and other organizations also use repositories to provide access to digitized special collections….”

Toward Reusable Science with Readable Code and Reproducibility

Abstract:  An essential part of research and scientific communication is researchers’ ability to reproduce the results of others. While there have been increasing standards for authors to make data and code available, many of these files are hard to re-execute in practice, leading to a lack of research reproducibility. This poses a major problem for students and researchers in the same field who cannot leverage the previously published findings for study or further inquiry. To address this, we propose an open-source platform named RE3 that helps improve the reproducibility and readability of research projects involving R code. Our platform incorporates assessing code readability with a machine learning model trained on a code readability survey and an automatic containerization service that executes code files and warns users of reproducibility errors. This process helps ensure the reproducibility and readability of projects and therefore fast-track their verification and reuse.


The Code4Lib Journal – Introducing SAGE: An Open-Source Solution for Customizable Discovery Across Collections

Abstract:  Digital libraries at research universities make use of a wide range of unique tools to enable the sharing of eclectic sets of texts, images, audio, video, and other digital objects. Presenting these assorted local treasures to the world can be a challenge, since text is often siloed with text, images with images, and so on, such that per type, there may be separate user experiences in a variety of unique discovery interfaces. One common tool that has been developed in recent years to potentially unite them all is the Apache Solr index. Texas A&M University (TAMU) Libraries has harnessed Solr for internal indexing for repositories like DSpace, Fedora, and Avalon. Impressed by frameworks like Blacklight at peer institutions, TAMU Libraries wrote an analogous set of tools in Java, and thus was born SAGE, the Solr AGgregation Engine, with two primary functions: 1) aggregating Solr indices or “cores,” from various local sources, and 2) presenting search facility to the user in a discovery interface.


F-UJI Automated FAIR Data Assessment Tool | FAIRsFAIR

“The F-UJI assessment is based on 16 out of 17 core FAIR object assessment metrics developed within FAIRsFAIR and each corresponding to a part or the whole of a FAIR principle. F-UJI adheres to existing web standards and PID resolution services best practices and utilises external registries and resources such as re3data1 and Datacite2 APIs, SPDX License List3, RDA Metadata Standards Catalog4, and Linked Open Vocabularies (LOV)5   For information on the practical tests implemented against the metrics, see Devaraju, Huber, et al., 2020.

The source code is now available with a free license through Github. Any feedback on improving the tool and associated metrics can be added as an issue on Github. …”

CU Boulder to host ‘Radical Open Access: Experiments in (Post-)Publishing Symposium’ | University Libraries | University of Colorado Boulder

“With the demise of traditional gatekeepers, we are witnessing the rapid rise of alternative modes of both scholarly publishing and distribution as well as the artistic exhibition of computer generated works of art in digital environments. 

The maturation of open access and collaborative platforms are in fact blurring the distinctions between publishing as a significant force of cultural activity in both contemporary art and leading-edge academic venues.

In this context, the symposium will question the current corporatized systems of academic publishing and the commercial-driven art museum and upmarket gallery systems, as well as serve as a forum to interrogate new models of collective action for collaborating on, creating and sharing scholarship and art. Following the symposium will be a “Clinic for Open Source Arts,” for a conversation about open source digital tools for creativity….”

Open Publishing Fest 2021: November 08-19, 2021. Call for proposals now open!

Open Publishing Fest is a decentralized public event that brings together communities supporting open source software, open content, and open publishing models.

Held over two weeks in November this year, Open Publishing Fest will feature discussions, demos, and performances that showcase our paths toward a more open world.

Open Knowledge ?/= Open Publishing ?

For more info or to discuss ideas please email

Sci-Hub Celebrates 10 Years Of Existence, With A Record 88 Million Papers Available, And A Call For Funds To Help It Add AI And Go Open Source | Techdirt

“To celebrate ten years offering a large proportion of the world’s academic papers for free — against all the odds, and in the face of repeated legal action — Sci-Hub has launched a funding drive:

Sci-Hub is run fully on donations. Instead of charging for access to information, it creates a common pool of knowledge free for anyone to access.

The donations page says that “In the next few years Sci-Hub is going to dramatically improve”, and lists a number of planned developments. These include a better search engine, a mobile app, and the use of neural networks to extract ideas from papers and make inferences and new hypotheses. Perhaps the most interesting idea is for the software behind Sci-Hub to become open source. The move would address in part a problem discussed by Techdirt back in May: the fact that Sci-Hub is a centralized service, with a single point of failure. Open sourcing the code — and sharing the papers database — would allow multiple mirrors to be set up around the world by different groups, increasing its resilience….”