Towards FAIR principles for research software | Data Science

Abstract:  The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility, interoperability and reusability of digital research objects for both humans and machines. Until now the FAIR principles have been mostly applied to research data. The ideas behind these principles are, however, also directly relevant to research software. Hence there is a distinct need to explore how the FAIR principles can be applied to software. In this work, we aim to summarize the current status of the debate around FAIR and software, as a basis for the development of definite community-agreed principles for FAIR research software in the future. We discuss what makes software different from data with respect to the application of the FAIR principles, present an analysis of where the existing principles can directly be applied to software, where they need to be adapted or reinterpreted, and where the definition of additional principles is required. Furthermore, we discuss desired characteristics of research software that go beyond FAIR.


New Landscapes on the Road of Open Science: 6 key issues to address for research data management in the Netherlands | Open Working

“The road to Open Science is not a short one. As the chairman of the Executive Board of the European Open Science Cloud, Karel Luyben, is keen to point out, it will take at least 10 or 15 years of travel until we reach a point where Open Science is simply absorbed into ordinary, everyday science.

Within the Netherlands, and for research data in particular, we have made many strides towards that final point. We have knowledge networks such as LCRDM, a suite of archives covered by the Research Data Netherlands umbrella, and the groundbreaking work done by the Dutch Techcentre for Life Sciences.

But there is still much travel to be done; many new landscapes to be traversed. Data sharing is still far from being the norm (see here for a visualisation of these results).

The authors of this blog post have put together six areas that, in their opinion, deserve attention on our Open Science journey….”

The fundamental problem blocking open access and how to overcome it: the BitViews project

Abstract:  In our view the fundamental obstacle to open access (OA) is the lack of any incentive-based mechanism that unbundles authors’ accepted manuscripts (AMs) from articles (VoRs). The former can be seen as the public good that ought to be openly accessible, whereas the latter is owned by publishers and rightly paywall-restricted. We propose one such mechanism to overcome this obstacle: BitViews. BitViews is a blockchain-based application that aims to revolutionize the OA publishing ecosystem. Currently, the main academic currency of value is the citation. There have been attempts in the past to create a second currency whose measure is the online usage of research materials (e.g. PIRUS). However, these have failed due to two problems. Firstly, it has been impossible to find a single agency willing to co-ordinate and fund the validation and collation of global online usage data. Secondly, online usage metrics have lacked transparency in how they filter non-human online activity. BitViews is a novel solution which uses blockchain technology to bypass both problems: online AMS usage will be recorded on a public, distributed ledger, obviating the need for a central responsible agency, and the rules governing activity-filtering will be part of the open-source BitViews blockchain application, creating complete transparency. Once online AMS usage has measurable value, researchers will be incentivized to promote and disseminate AMs. This will fundamentally re-orient the academic publishing ecosystem. A key feature of BitViews is that its success (or failure) is wholly and exclusively in the hands of the worldwide community of university and research libraries, as we suggest that it ought to be financed by conditional crowdfunding, whereby the actual financial commitment of each contributing library depends on the total amount raised. If the financing target is not reached, then all contributions are returned in full and if the target is over-fulfilled, then the surplus is returned pro rata.

Meet Plume: A new PubSweet platform created by the French Financial Jurisdictions : Collaborative Knowledge Foundation

“The French financial jurisdictions, which include the Paris-based Cour des comptes (the French Superior Audit Institution) and the regional and territorial chambers of accounts, have been collaborating with Coko for the past 10 months, building an experimental PubSweet platform.

The project is part of a program called Public Interest Entrepreneurs, directed by Etalab, a department of the French Interministerial Directorate for Digital Affairs that promotes open data and open source. The project is headed up by two public interest entrepreneurs, Nikos Peteinatos, designer and member of the Editoria Advisory Group, and Erica Marco, developer.

The system, currently under development, is called Plume, and it leverages the PubSweet framework and community modules, including Editoria, Wax and Paged.js (from the forthcoming Cabbage Tree Labs). The pilot phase of the project ran for ten months, and deemed successful, the team now embarks on a secondary phase over the next six months with two new developers joining the team….

The system’s primary function is to facilitate the authoring of audit reports. It can be thought of as a customized version of Editoria….”

“Make sharing in your repository the simplest way to increase your author’s impact.

Sharing should be simple. We make sure that deposit into your repository means only dragging and dropping a paper by automatically doing all the hard work for depositors. It’ll be free, open source, community owned and easily set up in minutes….”

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

Abstract:  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.

Make code accessible with these cloud services

“Scientific software often requires installing, navigating and troubleshooting a byzantine network of computational ‘dependencies’ — the code libraries and tools on which each software module relies. Some have to be compiled from source code or configured just so, and an installation that should take a few minutes can degenerate into a frustrating online odyssey through websites such as Stack Overflow and GitHub. “One of the hardest parts of reproducibility is getting your computer set up in exactly the same way as somebody else’s computer is set up. That is just ridiculously difficult,” says Kirstie Whitaker, a neuroscientist at the Alan Turing Institute in London….”

Open is Eating the World: What Source Code and Science Have in Common – The Scholarly Kitchen

“There are increasingly noticeable connections between open source and open research. Both open research and open source are promoted as mechanisms to improve quality by creating faster and more robust feedback mechanisms, they’re both intended to reduce waste and unnecessarily duplicated effort (validation is not duplication of effort, they’re different things), and they both draw / are dependent on communities to be both valuable and sustainable….”