Agile Research Data Management with Open Source: LinkAhead

Authors : Daniel Hornung, Florian Spreckelsen, Thomas Weiß

Research data management (RDM) in academic scientific environments increasingly enters the focus as an important part of good scientific practice and as a topic with big potentials for saving time and money. Nevertheless, there is a shortage of appropriate tools, which fulfill the specific requirements in scientific research.

We identified where the requirements in science deviate from other fields and proposed a list of requirements which RDM software should answer to become a viable option. We analyzed a number of currently available technologies and tool categories for matching these requirements and identified areas where no tools can satisfy researchers’ needs.

Finally we assessed the open-source RDMS (research data management system) LinkAhead for compatibility with the proposed features and found that it fulfills the requirements in the area of semantic, flexible data handling in which other tools show weaknesses.

URL : Agile Research Data Management with Open Source: LinkAhead


The Rise of GitHub in Scholarly Publications

Authors : Emily Escamilla, Martin Klein, Talya Cooper, Vicky Rampin, Michele C. Weigle, Michael L. Nelson

The definition of scholarly content has expanded to include the data and source code that contribute to a publication. While major archiving efforts to preserve conventional scholarly content, typically in PDFs (e.g., LOCKSS, CLOCKSS, Portico), are underway, no analogous effort has yet emerged to preserve the data and code referenced in those PDFs, particularly the scholarly code hosted online on Git Hosting Platforms (GHPs).

Similarly, the Software Heritage Foundation is working to archive public source code, but there is value in archiving the issue threads, pull requests, and wikis that provide important context to the code while maintaining their original URLs. In current implementations, source code and its ephemera are not preserved, which presents a problem for scholarly projects where reproducibility matters.

To understand and quantify the scope of this issue, we analyzed the use of GHP URIs in the arXiv and PMC corpora from January 2007 to December 2021. In total, there were 253,590 URIs to GitHub, SourceForge, Bitbucket, and GitLab repositories across the 2.66 million publications in the corpora.

We found that GitHub, GitLab, SourceForge, and Bitbucket were collectively linked to 160 times in 2007 and 76,746 times in 2021. In 2021, one out of five publications in the arXiv corpus included a URI to GitHub.

The complexity of GHPs like GitHub is not amenable to conventional Web archiving techniques. Therefore, the growing use of GHPs in scholarly publications points to an urgent and growing need for dedicated efforts to archive their holdings in order to preserve research code and its scholarly ephemera.


The Labor of Maintaining and Scaling Free and Open-Source Software Projects

Authors : Richard Geiger, Dorothy Howard, Lilly Irani

Free and/or open-source software (or F/OSS) projects now play a major and dominant role in society, constituting critical digital infrastructure relied upon by companies, academics, non-profits, activists, and more. As F/OSS has become larger and more established, we investigate the labor of maintaining and sustaining those projects at various scales.

We report findings from an interview-based study with contributors and maintainers working in a wide range of F/OSS projects. Maintainers of F/OSS projects do not just maintain software code in a more traditional software engineering understanding of the term: fixing bugs, patching security vulnerabilities, and updating dependencies.

F/OSS maintainers also perform complex and often-invisible interpersonal and organizational work to keep their projects operating as active communities of users and contributors. We particularly focus on how this labor of maintaining and sustaining changes as projects and their software grow and scale across many dimensions.

In understanding F/OSS to be as much about maintaining a communal project as it is maintaining software code, we discuss broadly applicable considerations for peer production communities and other socio-technical systems more broadly.

URL : The Labor of Maintaining and Scaling Free and Open-Source Software Projects

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Assessing Open Source Journal Management Software

Author : Stewart Baker

The long-term sustainability of Open Source (OS) software depends on its community of developers and core users, as well as that community’s stability. Assessing OS software and the community which creates it is, therefore, an essential step in using OS software for a project.

In this study, surveys of OS journal management systems were reviewed to determine which were still actively maintained. Actively maintained systems were rated using QualiPSo’s Open Maturity Model (OMM), an assessment tool for determining the maturity and robustness of OS software. Of the OS journal management systems mentioned in existing surveys, only Ambra, Lodel, and Open Journal Systems (OJS) are still actively maintained.

Of these, OJS scored the highest OMM rating, followed by Ambra and Lodel. A new system, Janeway, was also assessed. Although OS software can carry risks, it also brings benefits to librarians, readers, and publishers of scholarly journals.

Assessing OS software and getting involved in OS software communities both help ensure the long-term survival of these communities and their work.

Publishing computational research — A review of infrastructures for reproducible and transparent scholarly communication

Authors : Markus Konkol, Daniel Nüst, Laura Goulier

Funding agencies increasingly ask applicants to include data and software management plans into proposals. In addition, the author guidelines of scientific journals and conferences more often include a statement on data availability, and some reviewers reject unreproducible submissions.

This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.

Still, publishing reproducible articles is a demanding task and not achieved simply by providing access to code scripts and data files. Consequently, several projects develop solutions to support the publication of executable analyses alongside articles considering the needs of the aforementioned stakeholders.

The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results. We compare the approaches across properties relevant for the involved stakeholders, e.g., provided features and deployment options, and also critically discuss trends and limitations.

The review can support publishers to decide which system to integrate into their submission process, editors to recommend tools for researchers, and authors of scientific papers to adhere to reproducibility principles.


Open Practices and Resources for Collaborative Digital Pathology

Author : Raphaël Marée

In this paper, we describe open practices and open resources in the field of digital pathology with a specific focus on approaches that ease collaboration in research and education settings.

Our review includes open access journals and open peer review, open-source software (libraries, desktop tools, and web applications), and open access collections. We illustrate applications and discuss current limitations and perspectives.

URL : Open Practices and Resources for Collaborative Digital Pathology


Open Systems Pharmacology community – an open access, open source, open science approach to modeling and simulation in pharmaceutical sciences

Authors : Jörg Lippert, Rolf Burghaus, Andrea Edginton, Sebastian Frechen, Mats Karlsson, Andreas Kovar, Thorsten Lehr, Peter Milligan, Valerie Nock, Sergej Ramusovic, Matthew Riggs, Stephan Schaller, Jan Schlender, Stephan Schmidt, Michaël Sevestre, Erik Sjögren, Juri Solodenko, Alexander Staab, Donato Teutonico

Systems Pharmacology integrates structural biological and pharmacological knowledge and experimental data enabling dissection of organism and drug properties and providing excellent predictivity.

The development of systems pharmacology models is a significant task requiring massive amounts of background information beyond individual trial data. Qualification of models needs repetitive demonstration of successful predictions.

Open Systems Pharmacology is a community that develops, qualifies and shares professional open source software tools and models in a collaborative open science way.