The case for free and open source software in research and scholarship

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today. This article is part of the theme issue ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico ’.

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The case for free and open source software in research and scholarship

10.31235/osf.io/ye7sx ◽

2020 ◽

Author(s):

Laura Fortunato ◽

Mark Galassi

Keyword(s):

Open Source ◽

Open Source Software ◽

Research Process ◽

Open Science ◽

Academic Community ◽

Original Form ◽

Academic Settings ◽

The Common ◽

Quality Of Research

Free and open source software (FOSS) is any computer program distributed under a licence that grants the user rights to run the program for any purpose, to study it, to modify it, and to redistribute it either in its original form or modified.We explore the close ties between FOSS and academia, and in particular the intersection with computational reproducibility. We begin by situating FOSS in relation to other open initiatives in academic settings — namely open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for researchers in any field, and anyone in the academic community concerned with the quality of research and its sustainability. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, using the GNU Scientific Library as a case study.We conclude by discussing why the common interpretation of “open source” as “open code” is misplaced, and we use this example to further articulate the case for free and open source software in research and scholarship.

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Ways to Open Science. Open Research Infrastructures and the role of repositories

Septentrio Conference Series ◽

10.7557/5.3865 ◽

2016 ◽

Author(s):

Susanne Blumesberger

Keyword(s):

Open Access ◽

Open Source ◽

Peer Review ◽

Open Source Software ◽

Peer Review Process ◽

Open Science ◽

Free Access ◽

Data Types ◽

Access Policies

Watch the VIDEO of the presentation.The Way to Open Science contains many components. One of these components would be open repositories based on open source software with free access to researchers. Open access policies are essential, as are open infrastructures and open contents. Repositories can support this openness by offering open licenses, open metadata , the possibility to use open formats and open thesauri. Another principal point is transparency. Open peer review should be possible, and the description of processes should also be transparent. Of course, an open license should provide all data types and metadata as well.It is important to help researchers to make their results visible and accessible and to encourage them to publish in OA-Journals and use repositories for the underlying data. Open Access Policies are supporting these efforts. Open data can be freely used, modified, and shared by anyone for any purpose. In order to do so, Open Licenses are required.Also Metadata are important components of the Way to Open Science. Metadata are data about data which should be free of all restrictions on access, structured and based on standards.Open formats are defined by a published specification and are not restricted in their use. They are mainly used by open-source software. Open Thesauruses are freely accessible for everyone without costs and with a free license.Open Processes should be documented, transparent, repeatable and reusable.An open peer review process is also a step forward to Open Science. Authors and referees are no longer anonymous. The whole process and the decision letters are open.Of course Open licenses allow the reuse of any work or data without any restrictions.The lecture will deal with various aspects of open science and focus on the role of repositories – with all chances and challenges.

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Q Methodology in the COVID-19 Era

Healthcare ◽

10.3390/healthcare9111491 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1491

Author(s):

Ahmed S. Alanazi ◽

Heather Wharrad ◽

Fiona Moffatt ◽

Michael Taylor ◽

Muhammad Ladan

Keyword(s):

Open Source ◽

Open Source Software ◽

Q Methodology ◽

Critical Time ◽

Research Process ◽

Structured Interviews ◽

Face To Face ◽

Secure Environment ◽

User Friendly

All face-to-face studies were affected by the COVID-19 pandemic, as they could not be run in person due to rules and guidance linked to social distancing which were in force during the outbreak. Finding and testing an available COVID-secure approach for both participants and researchers was important as was the need to continue conducting such studies during this critical time. At present, the extant literature indicates a clear gap in research that elucidates how to carry out a Q methodology study online, step by step. This paper describes an option for online Q methodology using an approach that simulates all of the steps performed in a face-to-face setting using an open-source software known as Easy-HtmlQ. Using a case study in telemedicine adoption as illustration, this paper also considers the perspective of both research participants and Q methodology researchers via semi-structured interviews. Using Easy-HtmlQ V1.1 in online Q methodology studies appears to be an affordable, practical and user-friendly solution. Some of the benefits associated with running Q methodology studies online were the decreased costs, enabling the recruitment of wider number of participants, providing a COVID-19-secure environment and offering convenience to both participants and researchers during the research process. The findings of this study may contribute to increasing the number of online Q methodology studies in the future, as it has succeeded in offering a feasible approach for Q methodology researchers.

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An Open Science Workflow for More Credible, Rigorous Research

10.31234/osf.io/wu6sn ◽

2021 ◽

Author(s):

Katherine S. Corker

Keyword(s):

Research Team ◽

Open Data ◽

Ways Of Knowing ◽

Research Process ◽

Open Science ◽

Research Quality ◽

Science Practices ◽

Open Research ◽

Rigorous Research

Part of what distinguishes science from other ways of knowing is that scientists show their work. Yet when probed, it turns out that much of the process of research is hidden away: in personal files, in undocumented conversations, in point-and-click menus, and so on. In recent years, a movement towards more open science has arisen in psychology. Open science practices capture a broad swath of activities designed to take parts of the research process that were previously known only to a research team and make them more broadly accessible (e.g., open data, open analysis code, pre-registration, open research materials). Such practices increase the value of research by increasing transparency, which may in turn facilitate higher research quality. Plus, open science practices are now required at many journals. This chapter will introduce open science practices and provide plentiful resources for researchers seeking to integrate these practices into their workflow.

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BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference

F1000Research ◽

10.12688/f1000research.74074.1 ◽

2021 ◽

Vol 10 ◽

pp. 1054

Author(s):

Nomi L. Harris ◽

Peter J. A. Cock ◽

Christopher J. Fields ◽

Karsten Hokamp ◽

Jessica Maia ◽

...

Keyword(s):

Molecular Biology ◽

Computational Biology ◽

Open Source ◽

Open Source Software ◽

Intelligent Systems ◽

Open Science ◽

Global Perspectives ◽

The Galaxy ◽

Bioinformatics Community

The 22nd annual Bioinformatics Open Source Conference (BOSC 2021, open-bio.org/events/bosc-2021/) was held online as a track of the 2021 Intelligent Systems for Molecular Biology / European Conference on Computational Biology (ISMB/ECCB) conference. Launched in 2000 and held every year since, BOSC is the premier meeting covering topics related to open source software and open science in bioinformatics. In 2020, BOSC partnered with the Galaxy Community Conference to form the Bioinformatics Community Conference (BCC2020); that was the first BOSC to be held online. This year, BOSC returned to its roots as part of ISMB/ECCB 2021. As in 2020, the Covid-19 pandemic made it impossible to hold the conference in person, so ISMB/ECCB 2021 took place as an online meeting attended by over 2000 people from 79 countries. Nearly 200 people participated in BOSC sessions, which included 27 talks reviewed and selected from submitted abstracts, and three invited keynote talks representing a range of global perspectives on the role of open science and open source in driving research and inclusivity in the biosciences, one of which was presented in French with English subtitles.

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On everyday academic research

Voprosy Ekonomiki ◽

10.32609/0042-8736-2017-9-98-134 ◽

2017 ◽

pp. 98-134 ◽

Cited By ~ 1

Author(s):

J. Tirole

Keyword(s):

Common Good ◽

Academic Research ◽

Research Quality ◽

Economic Research ◽

Relevant Research ◽

The Common ◽

Verification Of Models ◽

Science And Research

In the fourth chapter of the book “The economy of the common good”, the nature of economics as a science and research practices in their theoretical and empirical aspects are discussed. The author considers the processes of modeling, empirical verification of models and evaluation of research quality. In addition, the features of economic cognition and the role of mathematics in economic research are analyzed, including the example of relevant research in game theory and information theory.

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