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.

URL : https://arxiv.org/abs/2001.00484

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

DOI : https://doi.org/10.3389/fmed.2019.00255

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.

DOI : https://doi.org/10.1002/psp4.12473

Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

Authors : Christina B. Reimer, Zhang Chen, Carsten Bundt, Charlotte Eben, Raquel E. London, Sirarpi Vardanian

The present paper is the mission statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab regarding Open Science. As early-career researchers (ECRs) in the lab, we first state our personal motivation to conduct research based on the principles of Open Science.

We then describe how we incorporate four specific Open Science practices (i.e., Open Methodology, Open Data, Open Source, and Open Access) into our scientific workflow. In more detail, we explain how Open Science practices are embedded into the so-called ‘co-pilot’ system in our lab.

The ‘co-pilot’ researcher is involved in all tasks of the ‘pilot’ researcher, that is designing a study, double-checking experimental and data analysis scripts, as well as writing the manuscript.

The lab has set up this co-pilot system to increase transparency, reduce potential errors that could occur during the entire workflow, and to intensify collaborations between lab members.

Finally, we discuss potential solutions for general problems that could arise when practicing Open Science.

URL : Open Up – the Mission Statement of the Control of Impulsive Action (Ctrl-ImpAct) Lab on Open Science

DOI : http://doi.org/10.5334/pb.494

The rising tide: Open source’s steady transformation

Authors : Matt Germonprez, Jonathan Lipps, Sean Goggins

Open source projects are transforming. Today, work within open source projects has come to be influenced by a growing set of companies and individuals who receive financial remuneration for their engagement.

As such, there is a central focus on commoditization and commercialization of open source products, which drives a trend towards a concealment of the various inner workings that produce these products.

Within this shift, the product becomes a central aim of open source project engagement, and the means of production becomes incidental.

In this paper, we explore the HCI research and design implications of the transformation of open source projects as part of commercial work and how we can come to better understand and protect the rising tide of open source projects.

DOI : https://doi.org/10.5210/fm.v24i8.9297

Online division of labour: emergent structures in Open Source Software

Authors : María J. Palazzi, Jordi Cabot, Javier Luis Cánovas Izquierdo, Albert Solé-Ribalta, Javier Borge-Holthoefer

The development Open Source Software fundamentally depends on the participation and commitment of volunteer developers to progress. Several works have presented strategies to increase the on-boarding and engagement of new contributors, but little is known on how these diverse groups of developers self-organise to work together.

To understand this, one must consider that, on one hand, platforms like GitHub provide a virtually unlimited development framework: any number of actors can potentially join to contribute in a decentralised, distributed, remote, and asynchronous manner.

On the other, however, it seems reasonable that some sort of hierarchy and division of labour must be in place to meet human biological and cognitive limits, and also to achieve some level of efficiency.

These latter features (hierarchy and division of labour) should translate into recognisable structural arrangements when projects are represented as developer-file bipartite networks.

In this paper we analyse a set of popular open source projects from GitHub, placing the accent on three key properties: nestedness, modularity and in-block nestedness -which typify the emergence of heterogeneities among contributors, the emergence of subgroups of developers working on specific subgroups of files, and a mixture of the two previous, respectively.

These analyses show that indeed projects evolve into internally organised blocks. Furthermore, the distribution of sizes of such blocks is bounded, connecting our results to the celebrated Dunbar number both in off- and on-line environments.

Our analyses create a link between bio-cognitive constraints, group formation and online working environments, opening up a rich scenario for future research on (online) work team assembly.

URL : https://arxiv.org/abs/1903.03375

Les business models de l’édition open source : Le cas des logiciels

Authors : Amel Charleux, Anne Mione

Cette recherche identifie les business models (BM) mis en œuvre par les éditeurs de logiciels libres et open source. Ces modèles requièrent une approche originale des BM parce que la création de la valeur dépend de l’attractivité du projet auprès de contributeurs dont le nombre, la qualité et la diversité ne sont pas contrôlés.

Cette spécificité pose la question du partage d’une valeur qui ne peut pas être anticipée ni formellement négociée. Nous procédons à une analyse quantitative de près de 200 logiciels et réalisons une taxonomie par la méthode TwoStep Cluster. Nos résultats mettent au jour quatre BM, engagement, exploration, expertise et optimisation.

URL : https://journals.openedition.org/fcs/2088