TOPS OpenCore Ethos Template

>>>>> gd2md-html alert: ERRORs: 1; WARNINGs: 4; ALERTS: 8. <ul style="color: red; font-weight: bold"><li>See top comment block for details on ERRORs and WARNINGs. <li>In the converted Markdown or HTML, search for inline alerts that start with >>>>> gd2md-html alert: for specific instances that need correction.</ul> Links to alert messages:<a href="#gdcalert1">alert1</a> <a href="#gdcalert2">alert2</a> <a href="#gdcalert3">alert3</a> <a href="#gdcalert4">alert4</a> <a href="#gdcalert5">alert5</a> <a href="#gdcalert6">alert6</a> <a href="#gdcalert7">alert7</a> <a href="#gdcalert8">alert8</a> >>>>> PLEASE check and correct alert issues and delete this message and the inline alerts.<hr> # TOPS OpenCore Ethos Template **Zoom link: **[https://agu.zoom.us/j/96168945823?pwd=T3RFR0ZEN0VsSVpGRXlnaUVUQmxzdz09](https://agu.zoom.us/j/96168945823?pwd=T3RFR0ZEN0VsSVpGRXlnaUVUQmxzdz09) **Otter transcript: **[https://otter.ai/u/UwJoNBAdpDu5TPsy5muaULhO9b4](https://otter.ai/u/UwJoNBAdpDu5TPsy5muaULhO9b4) **Sprint Google drive: **[https://bit.ly/tops_sprint](https://bit.ly/tops_sprint) **Sprint prep and guide: ** **Github repo: **[https://github.com/learnopenscience](https://github.com/learnopenscience) **Lesson git repo:** [https://github.com/learnopenscience](https://github.com/learnopenscience) **Zotero collection for references: **[https://www.zotero.org/groups/4714787/opencore](https://www.zotero.org/groups/4714787/opencore) **Modules & members: **[https://github.com/nasa/Transform-to-Open-Science/blob/main/docs/Area2_Capacity_Sharing/OpenCore/OpenCore_leads.md](https://github.com/nasa/Transform-to-Open-Science/blob/main/docs/Area2_Capacity_Sharing/OpenCore/OpenCore_leads.md) --- ## Team Facilitators: Lauren, Brooks Module SMEs: Tomoko, Stephen, Mariana, Ismael, Miguel, Shamsuddeen, Amber Module lead: Yo Module content reviewer: Mayya Sundukova --- Most of the old non-lesson content has been moved to this doc: --- # Creating Lesson Materials ## What to Contribute * Learning outcomes (6 maximum) * Have a discussion about who your learners are and what their knowledge and conditions are before beginning your objectives. * Answer the question “what do I want someone to know or do as a result of completing this module?” * Answer the question “how will I know that someone has completed this module successfully” * Framed as “Upon completion of this module the learner will be able to…” completed from [Blooms Taxonomy](https://larryferlazzo.edublogs.org/2009/05/25/the-best-resources-for-helping-teachers-use-blooms-taxonomy-in-the-classroom/)’s knowledge, comprehension, and analysis segments. * Module outline (lessons) * Lesson narratives * Intro (300-500 words) * Prerequisite information or terms * Main (1,500-2,500 words) * Summary (300-500 words) * Self checks, assessments/evaluations, glossary terms, acronyms, and activities * **Example of lesson:** [https://learnopenscience.github.io/module-template/intro.html](https://learnopenscience.github.io/module-template/intro.html) * References are added to zotero * **Audience:** Focus on the basics, talking to many people that are not experts, from various disciplines, see example [here](https://docs.google.com/document/d/1XJjT5NOvpAlm7YwycM6qKh_FFlkguL6MtF0jRbQwt1o/edit#heading=h.2teoemvq6022) * Video and graphics will not be added at this stage but if you feel a certain area would benefit then indicate it, e.g. this would be great place for a video/infographic. Video is used to create context and connection, why is this material important to the learner, how will it help the learner apply the material taught or gain confidence. --- ## Lesson Anatomy * Each lesson ~30 mins, between 3000-4000 words * Between 2500-3000 words if we have 5 min video + 5 min assessment activity * Introduction - 1-3 paragraphs discussing the material and subtopics that will be covered in the lesson. This may include historical or positioning details, concept definitions, and transitions from the previous lesson. (300-500 words) * Main narrative - Written in paragraph form, should align with at least one of the defined learning objectives for the module. Please note concepts or content where examples, case studies, or stories may be included at the instructional design phase. (1,500-2,500 words, depending on size of lesson) * Summary - Generally 1–3 paragraphs reiterating the major concepts and points discussed in the narrative that the learner should have learned during that lesson. (300-500 words) --- ## Final Learning Outcomes List the six learning outcomes for your module below. Use these objectives to develop your lessons (note that you can have LESS than 6 lessons!) On completion of the Ethos of Open Science TOPS module, learners will be able to: --- ## Module Outline [TOC] 1. --- ## **Lessons** The formats below are to help you gather your thoughts, feel free to modify and adjust. ### Lesson 1: WHAT: Intro to Open Science: What is it and what does it promote? <table> <tr> <td>Lesson Outline <h4>Introduction</h4> This is the first lesson in the module on the Ethos of Open Science. We’ll start explaining what we mean by the word, “ethos”. Ethos is defined by Merriam-Webster as “the distinguishing character, sentiment, moral nature, or guiding beliefs of a person, group, or institution”. So this lesson is about what makes Open Science, as an approach to knowledge-production, unique or distinguishable from other scientific methods. Note that “ethos” is not exactly “ethics”, but it is a broad enough term to include the moral attitudes held by the individuals or institutions practicing open science. To make it clear that there is a moral element to this discussion, we speak of “responsible Open Science” going forward. The lesson introduces the concept of open science as a whole, by explaining the history underpinning open science, what open science is, and how it works. It then discusses different components of open science and the pillars that make them up. At the end of the lesson, students will have an understanding of the brief history of open science and its definition. Open science goes beyond publishing– it is a redefinition of scientific collaboration and output. It is a culture intended to promote science and its social impact. Open science creates new opportunities for different stakeholders including researchers, decision makers, and public participants. Open science increases study transparency, repeatability, reproducibility, and confirmation. We expand what these terms mean and why they matter throughout this module and later OpenCore modules. <h4>Context and Definition</h4> Science evolves through collaborative development of theories and practices that are open for others to learn and build on. Throughout the ages - whilst in some cases, education and science was out of reach for the general populace and may have been kept for a privileged few, there have been other educational and scientific resources that were purposefully made available for others to re-use. Think of how dictionaries and encyclopedias have been around for centuries specifically to share standards of knowledge. (<a href="https://oi.uchicago.edu/research/publications/assyrian-dictionary-oriental-institute-university-chicago-cad">The first</a> “dictionary” dates back over 3,000 years!) Libraries, in turn, have existed for millennia to serve as repositories of knowledge in diverse formats, from ancient tablets and scrolls, to the books we expect to see today. Public museums have also been around for some time and play the role of educating people, as well as maintaining archives for researchers to gain further insights from. Institutions and practices throughout the ages have facilitated humanity’s endless desire for knowledge. As far back as the Medieval era, we already find physicians being encouraged to review one another’s work to ensure it was carried out appropriately (Rogers, <a href="https://doi.org/10.1308/rcsann.2020.0214">2021</a>). Today, we call this practice “peer review”. And, during the Enlightenment, scientists formed networks with whom they shared their theories via hand-written letters, and the adoption of the printer allowed for the emergence of scientific institutes and journals (Green, <a href="https://www.wiley.com/network/societyleaders/open-science/an-illustrated-history-of-open-science">2017</a>; see Kherroubi Garcia et al., <a href="doi.org/10.5281/zenodo.5731452">2022</a>). However, open science has only become a distinct set of practices in recent decades. We can see open science as both being encouraged by social and technological developments, and responding to problems in the scientific process. The emergence of the internet and other digital technologies have more recently allowed for science to be conducted even more collaboratively. In 1971, <a href="https://www.gutenberg.org/about/background/history_and_philosophy.html">Project Gutenberg</a> started making books in the 📖public domain📖 available online. In 1987, we saw <a href="https://uh-ir.tdl.org/handle/10657/5149">the first open access </a>📖<a href="https://uh-ir.tdl.org/handle/10657/5149">journal</a>📖 being published. In 1991 the central storage platform arXiv was launched for the exchange of manuscripts in physics (though without 📖peer review📖) (Ginsparg, <a href="https://doi.org/10.1038/s42254-021-00360-z">2021</a>). However, these endeavors do not amount to open science in the sense we discuss it today. In recent years, we have learned of various issues in the scientific process that necessitate specific responses. Two such issues are the 📖replication crisis📖 (Fidler & Gordon, <a href="https://theconversation.com/science-is-in-a-reproducibility-crisis-how-do-we-resolve-it-16998">2013</a>; Elsherif et al., <a href="https://forrt.org/glossary/reproducibility-crisis-aka-replicab/">2021a</a>) and 📖publication bias📖 (Joober, et al., <a href="doi.org/10.1503/jpn.120065">2012</a>; Elsherif et al., <a href="https://forrt.org/glossary/publication-bias-file-drawer-proble/">2021</a>b). The replication crisis refers to scientific findings not being validated by other scientists’ efforts to replicate them. The publication bias amounts to the greater ease to publish scientific findings that only “very clearly” confirm or disprove hypotheses. Thus, open science captures both the spirit of making knowledge more accessible and responding to poor scientific practices. We will discuss more reasons why open science is important, both the personal benefits and as a public good, in 🔗Lesson 2 of this module, “Benefits and Challenges of responsible Open Science: Why does it matter?”🔗 <h4>Definitions of Open Science and responsible Open Science</h4> Formal definitions and governance mechanisms to ensure best practices in open science have emerged alongside the open science movement. <ul> <li>In 1997, <a href="https://publicationethics.org/about/our-organisation">COPE was established</a> and has since supported the fostering of responsible publishing culture. <li>The <a href="https://www.budapestopenaccessinitiative.org">2001 Budapest Open Access Initiative</a> provided a clear working definition of open access, one of the components of open science (as we will see shortly). <li>In 2012, the <a href="https://credit.niso.org">Contributor Role Taxonomy</a> was developed so that more diverse collaborators in research can be adequately credited for their work. <li>The <a href="http://doi.org/10.1242/dmm.012955">2013 Declaration on Research Assessment</a> then outlined best practices in the assessment of research. <li>In 2014, the <a href="https://ocsdnet.org/about-ocsdnet/">Open and Collaborative Science in Development Network</a> was established to enable open science approaches to developmental research for the Global South. <li>2014 also saw the launch of the <a href="https://force11.org/info/joint-declaration-of-data-citation-principles-final/">Data Citation Principles</a>, which advocate for – amongst other things – making data independently citable. <li>The <a href="https://www.go-fair.org/fair-principles/">2016 FAIR principles</a> emerged as a way to guide practices in open science, and enabled the implementation of the Data Citation Principles. <li>The <a href="https://www.gida-global.org/care">2018 CARE principles</a> established data governance practices for indigenous data and practices. In this complex context, we can draw on a few definitions of Open Science: “Open Science is transparent and accessible knowledge that is shared and developed through collaborative networks” (Vicente-Saez & Martinez-Fuentes, <a href="https://doi.org/10.1016/j.jbusres.2017.12.043">2018</a>). “Open science is [...] an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems (UNESCO, <a href="https://unesdoc.unesco.org/ark:/48223/pf0000379949.locale=en">2021</a>). Globally, Open Science is being valued and given importance as it recognizes disparities and regional differences, providing a framework to handle challenges and contribute to minimize knowledge, technological and digital differences between countries. For instance, when different researchers from across the globe are invited to research collaboratively, trust and novelty increases and as a result it improves quality, efficacy and responsiveness in research as being the benefits of Open Science. -- >Extra call-out box: (I don’t know what the right word for it is) Here are some other definitions of Open Science. Are there any more you would add? Open Science is a practice for increasing the accessibility and transparency of scientific research. The concept of Open Science is built around shared principles such as inclusion, fairness, equity, & sharing (Zee & Reich, <a href="https://doi.org/10.1177/2332858418787466">2018</a>). An umbrella term reflecting the idea that scientific knowledge of all kinds, where appropriate, should be openly accessible, transparent, rigorous, reproducible, replicable, accumulative, and inclusive, all which are considered fundamental features of the scientific endeavor. Open science consists of principles and behaviors that promote transparent, credible, reproducible, and accessible science. Open science has six major aspects: open data, open methodology, open source, open access, open peer review, and open educational resources. (FORRT open science glossary, <a href="https://forrt.org/glossary/open-science/">https://forrt.org/glossary/open-science/</a>) <h4>Open Science aspects</h4> Open science has various components: open access, open access journals, open peer review, open research data, open source, open science policies, with use of open licensing, open software for reproducible research, among others (Open Science Basics, retrieved from <a href="https://open-science-training-handbook.gitbook.io/book/open-science-basics">https://open-science-training-handbook.gitbook.io/book/open-science-basics</a>, 2022). The below image from Robinson (<a href="https://osaos.codeforscience.org/what-is-open/">2018</a>) captures some of the components of open science, although the list differs depending on who you ask (see Pontika et al., <a href="http://dx.doi.org/doi:10.1145/2809563.2809571">2015</a>). >>>>> gd2md-html alert: inline image link here (to images/image1.png). Store image on your image server and adjust path/filename/extension if necessary. (<a href="#">Back to top</a>)(<a href="#gdcalert2">Next alert</a>) >>>>> <img src="images/image1.png" width="" alt="alt_text" title="image_tooltip"> (Image from Robinson, <a href="https://osaos.codeforscience.org/what-is-open/">2018</a>; needs adapting in light of the list below) Open Science is an umbrella term that captures eight components. The below list helps us reflect on the ambition that drives the open science movement. In short, open science is not limited to a discipline or a particular aspect of scholarly practice. Rather, open science seeps into every practice of scholarly work. <ul> <li>Open Access refers to making research methods, data and outputs accessible by default, where advisable; this is touched on in lesson five below. <li>Open Data relates to making data used in science accessible for others to study, re-usable for other pertinent projects, and available for redistribution. More on this topic will be discussed in the module Open Data. <li>Open Software is about making the source code of software transparent, allowing people to collaborate on its improvement; more will be said in the module Open Software. <li>Open Tools & Resources are those that have been developed precisely to facilitate open science practices, from open hardware and online toolkits to behavioral guidelines; learn more in the module Open Tools & Resources. <li>Open Results is a broad term capturing open access, open data and open software, as it is about making results from all stages of a research lifecycle open, including their evaluation, which should not be limited to traditional peer review; learn more in the module Open Results. <li>Open Educational Resources are learning and teaching materials made available through 📖<a href="https://forrt.org/glossary/open-licenses/">open licenses</a>📖 that permit no-cost access, re-use, re-purpose, adaptation and redistribution by others (see <a href="https://www.unesco.org/en/communication-information/open-solutions/open-educational-resources">UNESCO’s explainer</a>); note that the present TOPS OpenCore is an example of such a resource! <li>Equity, Diversity, Accessibility and Inclusion are crucial values for the growth and sustainability of open science practices, as they foster the wellbeing of open science practitioners and communities. Shared principles about responsible scientific outputs also shape the behaviors of open science communities, with codes of conduct as a mechanism to ensure inclusive practices (see the following component of open science). <li>Open Community Practices refers to the fact that open science is conducted by communities of practitioners that foster collaborative working environments, beyond disciplinary boundaries and professions; this is touched on when discussing stakeholders in lesson three of this module. <h4>There is no one ethos</h4> It is important to note that there is no one unique way of practicing or conducting open science. The outlined categories show us the diversity of practices involved in open science. Research has also shown that there are at least five schools of thought in open science, each one holding different assumptions and striving for different goals (Fecher & Friesike, <a href="https://doi.org/10.1007/978-3-319-00026-8_2">2013</a>): >>>>> gd2md-html alert: inline image link here (to images/image2.png). Store image on your image server and adjust path/filename/extension if necessary. (<a href="#">Back to top</a>)(<a href="#gdcalert3">Next alert</a>) >>>>> <img src="images/image2.png" width="" alt="alt_text" title="image_tooltip"> Diverse practices, assumptions and goals are just part of the complexity of open science. There are also divergent moral principles guiding open science communities. Such principles are captured in 📖codes of conduct📖. A code of conduct is a community governance mechanism that outlines the principles and practices expected of a given research community’s members, as well as the process for investigating and reprimanding those in violation of the code. In a sense, a code of conduct constitutes the moral backbone of a research community. However, as with the numerous schools of thought, there are similarly many codes of conduct. In other words, there is no one set of universal principles that all open science practitioners abide by. For example, consider how <a href="https://openlifesci.org/code-of-conduct">OLS</a>, <a href="https://osf.io/6gsye">INOSC</a>, <a href="https://allea.org/portfolio-item/the-european-code-of-conduct-for-research-integrity-2/">allea</a>, <a href="https://www.agu.org/Plan-for-a-Meeting/AGUMeetings/Meetings-Resources/Meetings-code-of-conduct">AGU</a> and <a href="https://ethicalsource.dev/community-code-of-conduct/">Ethical Source</a> all have different codes of conducts and guiding principles. This great diversity responds to the growing proliferation of open science initiatives and the great use we can make of open science approaches to knowledge. One of the biggest driving forces is the effect of open science on the research performance. Indeed, some studies have even found that the best-performing universities are those that conduct science following open practices (see Huang et al., <a href="https://doi.org/10.7554/eLife.57067">2020</a>). More will be said in the following lesson about the benefits of open science and different stakeholders. For now, consider some of the regional policies encouraging open science: <ul> <li>The European Commission (<a href="https://data.europa.eu/doi/10.2777/121253">2017</a>) has outlined the skills and competencies researchers need to practise open science; <li>The National Academies of Sciences, Engineering and Medicine (<a href="https://doi.org/10.17226/25116">2018</a>) promotes open science by design as a vision for 21st century research; <li>UNESCO (<a href="https://unesdoc.unesco.org/ark:/48223/pf0000379949.locale=en">2021</a>) has developed a series of recommendations to ensure best open science practices, which are conducive to the United Nations’ <a href="https://sdgs.un.org/goals">Sustainable Development Goals</a>; <li>The European Open Science Cloud (EOSC) for finding and re-using data, and the Open Research Europe (ORE) publishing platform (European Commission, <a href="https://data.europa.eu/doi/10.2777/18252">2021</a>). Ultimately, open science practices guide approaches to knowledge-creation that best help confront the challenges of our era. Through this module and the wider TOPS curriculum, you can become a part of this impactful movement. <h4>Performing open science responsibly:</h4> Responsible Open Science is a term we use through the rest of the module. We define it as: considering open science as the core of your science project and maximizing ethical actions for open science to minimize current challenges (e.g. data sharing, inclusion, and accessibility). In responsible Open Science, the best possible and practical practices should be explored at the early stage of your science project. Here we share with you following rules of thumb: <ul> <li>Using best practices where possible <li>Being practical and realistic about resources available and pressures on open science practitioners <li>Not sharing things that shouldn’t be shared <li>Being inclusive of all people <h4>Summary</h4> In this lesson, we have learned a brief history of open science, its definition, and the ethos of open science and definition of responsible Open Science. Open science practices provide significant advantages relative to more traditional closed practices. However, there are still problems that must be addressed, which many view as obstacles to open science. In the next lesson, we will talk about the benefits of open science and its challenges. <h4> Further Reading: </h4> Below are some further readings regarding this module: <ol> <li><a href="https://link.springer.com/chapter/10.1007/978-3-319-00026-8_2">Open Science : One Term, Five Schools of Thought</a> <li><a href="https://elifesciences.org/articles/16800">How open science helps researchers succeed</a> <li><a href="https://nap.nationalacademies.org/read/26308/chapter/1">Developing a Toolkit for Fostering Open Science Practices: Proceedings of a Workshop</a> National Academies of Sciences, Engineering, and Medicine. 2021. <ol> <li>Reproducibility and Replicability in Science. Washington, DC: The National Academies Press. <a href="https://doi.org/10.17226/25303">https://doi.org/10.17226/25303</a> . <li>Open Science and Radical Solutions for Diversity, Equity and Quality in Research: A Literature Review of Different Research Schools, Philosophies and Frameworks and Their Potential Impact on Science and EducationGong, “Open Science.”<a href="https://doi.org/10.1177/20966083221091867">https://doi.org/10.1177/20966083221091867</a> <li>Book by Miedema, Open Science. <a href="https://doi.org/10.1007/978-94-024-2115-6">https://doi.org/10.1007/978-94-024-2115-6</a> Further reading on terms and definitions: <ol> <li>Open Science glossary from the FORRT (Framework for Open and Reproducible Research Training) <a href="https://forrt.org/glossary/open-science/">https://forrt.org/glossary/open-science/</a> </li> </ol> </li> </ol> </li> </ol> </li> </ul> </li> </ul> </li> </ul> </li> </ul> </td> </tr> <tr> <td> </td> </tr> </table> Questions/Reflection: ``` Questions for students of the course: How has research practice changed over the past few decades ? As a researcher how do different components of responsible Open Science transform knowledge contribution? We learned that there is "no one ethos" in this lesson. Can you explain what this means, and why? ``` --- ### ### Lesson 2: WHY: Benefits and Challenges of responsible Open Science: Why does it matter? >>>>> gd2md-html alert: Long single-cell table. Check to make sure this is meant to be a code block. (<a href="#">Back to top</a>)(<a href="#gdcalert4">Next alert</a>) >>>>> ``` Introduction In the previous lesson, we learned about foundational concepts that define Open Science. In this lesson, we address some benefits and challenges of working in the open. Here we aim to present a take on the development of science that's not only focused on scientific results but also on the process of creation, and the stakeholders that constitute the community. Stakeholders can be individuals producing scientific knowledge (i.e, researchers themselves), individuals consuming, applying and regulating scientific research (i.e., practitioners, general public, policy-makers, organizations, communities, etc.), and the larger scientific ecosystem (i.e., scientific journals, repositories, archives, etc.). We discuss more about the people who perform and benefit from open science - and how to support them - in Lesson 3. In this lesson, we highlight the various benefits of open science across multiple stakeholders, providing some examples that can be explored further. Further, challenges in adopting open science practices are explored. Benefits of Open Science Quality of research For researchers, a primary benefit of increased transparency and verifiability is that it allows readers and stakeholders to judge whether results presented are accurate (Chambers, & Tzavella, 2022) and, importantly, that the results are not produced by questionable research practices that lead to misleading or unreliable results (John et al., 2012). Open science practices assure that various statistical estimates of a study (e.g., p-values, effect sizes) can meaningfully be interpreted (Mayo, 2017; Cummings et al., 2016). And allows others to scrutinize the analytic decisions of the researchers, such as whether the analysis was planned before or after observing the data (Nosek et al., 2018). This allows others to check if they can arrive at the same conclusion as the original research team, and facilitates stronger public trust and support (UNESCO, 2021). Pull-out box: Real world implications of non-transparent science: The Free Software Foundation Europe (FSFE) provides a compelling position paper explaining why transparency is important for science. When computers are used to produce scientific research, the code is considered a "method", much like in a lab research setting, a set of instructions for working with cells or agar plates might be a method. Peer-reviewed methods are an essential step in the scientific process. When these steps are not shared, no-one else can reproduce the work, or build upon it for future scientific endeavors. It also allows people to judge whether or not the methods are trustworthy. In this case study, the FSFE reminds us of a time when closed methods were not trustworthy. Volkswagen revealed it intentionally programmed its diesel engines to cheat during laboratory emissions testing. This meant that people drove these cars thinking they were trustworthy and safer for the environment than they actually were. In this case, the real emissions from the engines were more than 40 times over the legal limit in the USA! Had the code for the diesel engines - the "scientific methods" - been open, it is possible that this untrustworthy behavior would have been picked up on much earlier. (Gkotsopoulou et al., 2017) https://download.fsfe.org/policy/letters/20170105-horizon2020-position-paper.pdf Quality and diversity of scholarly communications Furthermore, open science improves the state of scientific literature. Scientific journals have traditionally faced the severe issue of publication bias, where journal articles overwhelmingly feature novel and positive results (Devito & Goldacre, 2018). This results in a state where scientific results in certain disciplines published scientific results may have a number of exaggerated effects, or even be "false positives" (wrongly claiming that an effect exists), making it difficult to evaluate the trustworthiness of published results (Simmons et al., 2011; Nissen et al., 2016). Open science practices such as registered reports mitigate publication bias, and improve the trustworthiness of the scientific literature. Registered reports are journal publication formats that peer-review and accept articles before data collection is undertaken, eliminating the pressure to distort results (Chambers, & Tzavella, 2022). Other open science practices, such as 📖pre-registration📖 also allows allows a partial look into projects that for various reasons (such as lack of funding, logistical issues or shifts in organizational priorities) have not been completed or disseminated (Evans et al., 2021) giving these projects a publicly available output that can help inform about the current state of the field. Pull-out box: Not everything should be pre-registered: Pre-registration is the practice of registering your scientific study/experiment plans before you start the study. This helps to ensure that the experiment isn't changed part-way through if the results aren't the conclusion the researchers had hoped for, and can help ensure publication of "null results" which otherwise might not be published. Pre-registration is a good tool for hypothesis-driven science, when a researcher starts with a hypothesis, then proceeds to define steps (methods) to prove or disprove the hypothesis. Not all science is hypothesis-driven, though. Discovery driven science is more exploratory and doesn't usually start with a hypothesis. It may instead involve looking at existing data, or collecting more data, and trying to form conclusions based on the available evidence. Many domains perform discovery science, and generally these experiments and studies aren't suitable for pre-registration, since the exact direction of study may not be clear at the start of the research. Open Science is also a valuable tool to be used in the public sector. Movements like Public Money Public Code were started by people who believe in the value of having open research and data freely available to the population. Remarkable advances on the way we exerce democracy are also being empowered by science made on the open, software like Polis which leverages the concepts of Computational Democracy, empowers scientists to run statistics and machine learning technologies on opinions of millions of citizens. In other words, open science facilitates 📖citizen science📖. Response to societal challenges As science tackles consequential topics (climate change, pandemics and global health, democracy and misinformation), the transparency and verifiability of science is more important than ever. This is highlighted during the pandemic, where the creation of life-saving vaccines were spurred because the genomic sequence of SARS-CoV-2 was placed in GenBank, an open access database (Zastrow, 2020). Open science allows for rapid, global access and action especially for shared problems too difficult to solve by any one team alone. Responsible Open Science is not only beneficial - it can also be characterized as an ethical imperative, especially for publicly funded projects. UNESCO (2021), for example, writes "so as to ensure the human right to share in scientific advancement and its benefits, member states should establish and facilitate mechanisms for collaborative open science and facilitate sharing of scientific knowledge while ensuring other rights are respected" (pg. XX) The recent years have shown the great momentum of open science, with a number of funders, regulatory organizations and governing bodies mandating open science practices across various disciplines across the globe (e.g. European Commission; UNESCO, 2021; National Academies of Sciences, Engineering, and Medicine. 2018 ), with more details about it in Lesson 4 . The practicing scientist of today and especially of the future needs to learn about open science and start applying it into everyday practice. Less unnecessary repetition is better for study participants Open science, in a way, also gives back to the communities that scientists hope to serve. Through open science practices, research waste can be avoided, such as unintentional and costly repetition of previous studies (Lusoli and Glenos 2020). In the human sciences, this also reduces participant fatigue in the long term. By maximizing what is learned from publicly available data, one does not need to test repeatedly especially on already vulnerable communities. By "giving away" science, individuals, communities and organizations can more easily adopt research results to inform interventions for their own needs without the knowledge being gatekept by the original researchers and organizations involved. In this way, open science can facilitate strengthening the social and economic impacts of scientific results. Personal/career benefits Aside from accuracy, adhering to open science practices potentially offers personal career benefits to researchers themselves. Openly published research has a potential for greater visibility and impact by reaching larger audiences across the internet, leading to more citations and more like-minded collaborators and career/funding opportunities. (McKiernan et al., 2016). Open science practices can also enable stronger collaborations, both within and between disciplines (Hormia-Poutanen, & Forsström, 2016). The ease of access to open data brings new agents to the landscape allowing for broader and more diverse participation. Through open science practices, such as pre-registration, one allows for a stronger research design because feedback from various collaborators and stakeholders can be solicited before data collection begins. Similarly, preprints allow for speedier feedback on conclusions drawn from the data once it is collected. Pull-out box: Case study of a successful collaboration: Mozilla, an organization famous for the web browser Firefox, also runs a community-driven project called Common Voice. Common voice is an open crowd-sourced dataset of different voices and speech patterns, covering many different languages, accents, countries, and speech patterns. By making this data open and facilitating contributions from volunteers worldwide, speech recognition technology and text-to-speech technology is democratized and represents the members of the populace more equitably. Practicing open science with transparency, collegiality, and research integrity do require development of a whole set of technical and transferable "soft" skills, which would be extremely useful for researchers in their careers both in academic or non-academic sector. Some examples include digital content creation; information, publication, data literacy; communication and collaboration skills - we will come back to it in the bonus section of lesson 5. Therefore, It is important to have the training and mentoring widely offered to the researchers. Pull-out box: Short on time? Make sure to read the top-ten reasons to do open science at the end of this lesson for a quick TL;DR summary. Challenges in Open Science However, open science also comes with its challenges. Doing open science requires some extra effort from researchers to start and maintain, but its long-term benefits include a great overall increase in research efficiency, integrity, and public trust. For example, putting your code in the open will probably mean that some adjustments must be made, and sharing it with a community will demand that you choose how your contributions can be used by others. Sharing data can imply extra work and planning; however this organization and widespread discovery can greatly improve science and confidence in it. We will see more details on code sharing and licensing in the "How" lesson 5. In this lesson we focus on the challenges of your work, and the consequences of sharing - and in some cases, oversharing. . Not everything should be open - don't overshare without consent! In order to practice responsible Open Science, careful attention should be given to how data is anonymized and how sensitive information is removed from it in order to safeguard people's identity and to prevent various harms stemming from breach of privacy. In recent history, we have seen many cases of how the misuse of data and illicit means to collect it is harmful to the population. Scandals like the Facebook–Cambridge Analytica, and outrageous services selling very personal parts of users' lives without their knowledge and full consent are far too common. Preparing documentation, using standards, and creating metadata takes time and effort Additionally to treating users' data ethically, often further work is required to make research outputs not only publicly available but also understandable and accessible to various stakeholders. This means for example, that codes to be shared are understandable and properly documented. This might mean to have a testing system in place, make use of a distributed version control software and a CI/CD pipeline. If you're unfamiliar with any of these terms, don't worry! They will be covered in the "Open Software" module. (Maybe this last sentence is a cute little character with a balloon) Besides caring about code, if the project utilizes data and that's being open sourced, it might be necessary to also have documentation that adequately describes the data set's contents, nature and layout. This type of "data about data" is known as "📖metadata📖". It might also mean to tweak the formatting of the dataset to fit a specific pattern agreed by the broader community - this is known as using community-agreed data standards. Open community members don't always agree with each other Other than the more technical aspects of producing Open Science it's also important to keep in mind the societal aspects of the project. While interacting with the community can be one of the most fulfilling things about Open Science, it might also be a source of disagreements about the direction of the project or how it should be used. That's where licenses and codes of conduct come into place. By explicitly setting out rules for the community interactions and use of resources, licenses and codes of conduct are useful to both protect the maintainers and their vision of what the original project and the 📖forked📖 projects should comply with. Case scenarios in open communities As you saw in the last lesson the story of Open Software (which builds the foundation for Open Science) is vast and at times different open values can conflict deeply. Two particularly relevant movements that helped to shape our ideas and actions in Open Science today are the Open Source and the Free Software movement. The Open Source Initiative, an organization that advocates for Open Source, argues that Open Source code can't "discriminate against persons, groups, fields or endeavors", the Free Software movement affirms that "everyone should have the freedom to run the program as they wish, for any purpose ". Even though these maxims might sound very encompassing and welcoming there are several critics of the carelessness that these movements have been treating both maintainers and users of Open Source, as well as their gullible negligence on how powerful a tool code is and how it can be used to do evil. Speaking about doing evil, the Open Source Initiative addresses this problem with these exact words "Giving everyone freedom means giving evil people freedom, too". Recent movements like the Ethical Source and the First Do No Harm movements have been questioning the broadness of paradigms in which open resources are allowed to act, imposing ethical restrictions to the use of software through the use of licenses. There are also cases where the project maintainers took the lead and made their own licenses, such as for the data format JSON. Pull-out box: Examples of open science and open source that have been used for unintended purposes. ICE uses Chef-sugar (an open source project) [1] - an open source project being used by immigration enforcement authorities Illegal use of Elasticsearch branding by Amazon [2][3] All the "what's bad" essays on Stallman's website 📖Data Sovereignty📖, indigenous rights, and parachute/helicopter research: when marginalized people share their data, sometimes privileged researchers re-use the data without fair credit or funding reaching the original data creators. Further, science that is just "open" does not necessarily mean that it is of high quality. However, the transparency and verifiability that open science affords, makes readers and various stakeholders able to independently judge the trustworthiness of research products. Cultural barriers: not everyone wants to change, and institutions often move slowly A further challenge of adopting open science practices are institutional barriers to the researcher or practitioner. While one might be interested in adopting open science practices, they might lack support from their department or project supervisors and open science practices might not be given the budget, resources or time in a project cycle. Institutions might also not recognize open science practices in recruiting, training or promoting in the organization. These lack of incentives within organizations present difficult barriers to the adoption of open science. While there are many challenges to the adoption of open science, we believe that its various benefits and its ethical imperative to the self and to the scientific communities, citizens and policy-makers outweighs the cost of barriers. In addition, recognising the barriers and places where caution needs to be taken provides a first step towards resolving them. Summary Open Science provides benefits not only to society but also to the individuals who perform it. Walking the line between responsible appropriate sharing and irresponsible oversharing requires diligence but the path and the results of science made in the open are very rewarding to all its stakeholders. 10 Reasons to practice open science responsibly: responsible Open Science… … (including availability of data, code, materials, and early results) accelerates research broadly and greatly. … generates transparency and public trust and support … fosters working across and engaging multiple disciplines, or "convergent" science. … brings innovation through using big and aggregated data and information … supports public and community uses of science: also known as community science, participatory science, or citizen science. … helps fight misinformation and disinformation … is intentionally and thoughtfully inclusive practice … supports the key role of science in addressing major societal challenges in the 21st century (including climate change, sustainability) … makes your research more efficient and impactful and provides credit broadly responsible Open Science is the new normal,and regulatory and governing bodies are reaching a consensus toward pushing it). ``` Questions/Reflection: ``` Why are responsible Open Science practices important to a researcher's profile? How can a researcher benefit from responsible Open Science practices ? How does society benefit from responsible Open Science? In this lesson, we learned that responsible Open Science often takes time and requires diligence and dedication of researchers. Can you explain how and why? ``` --- ### ### Lesson 3: WHO: Stakeholders of Open Science: Who practices responsible Open Science and for whom? >>>>> gd2md-html alert: Long single-cell table. Check to make sure this is meant to be a code block. (<a href="#">Back to top</a>)(<a href="#gdcalert5">Next alert</a>) >>>>> ``` Introduction In previous lessons, we learned about the concept and motivation and aspiration of open science. Now let's think about "who" is practicing open science and for whom. In the first section of this lesson we dive deeper into understanding who the stakeholders for Open Science are. In the second part we cover essential topics about barriers to participation, and to include diverse stakeholders in open science communities and ways to overcome them. In this module we offer you a person-centered approach to making open science happen. Our intention is to prevent harmful consequences of science's misuse (even unintentional misuses) and to increase the impact of science, by leveraging other researchers' works and improving society. Who performs and benefits from open science? Stakeholders partaking in open science: As briefly discussed in previous lessons, Open science doesn't only concern researchers; many other stakeholders are affected by the outcomes of open science as well. Stakeholders are any individuals who can affect or be affected by open science projects. Although there are different ways to categorize stakeholders depending on your science projects, mainly there are three large groups; 1. Researchers, 2. Public, and 3. Policy-makers. Researchers Organizations Research Teams General public Decision Makers (regulatory, funding bodies, etc) Government Researchers: Individuals engaged in creating new knowledge (e.g. researchers, students, faculty staff at universities, researcher centers, researchers at libraries). Responsible for creating an open science environment as well as open outputs and processes. Public: Lay people who can drive/improve/conduct science (i.e. people who may not have an academic background or research experience). This may also be referred to as "citizen science", but you do not have to be a citizen of any particular country in order to participate in science! Policy-makers: Those with decision-making power (e.g. government, regulatory bodies) How each group contributes to Open Science Let's take a look at these groups, how they can contribute to open science (input) and what benefits they experience from open science (this was also discussed in Lesson 2). Note that overlap among researchers, the general public, and policy-makers can happen. Researchers' contribution to open science manifests by sharing and communication their research via open access publications (more about it in the Lesson How and Module Open Results) As a result, community of researchers benefits from increased visibility and credit, reproducibility, access to more data and attraction of funding, reduced work's duplication, conservation of resources and increased accessibility The general public contributes to open science research by above mentioned "citizen science" projects, as e.g. as volunteers to collect or manage (e.g. categorize) some type of data. As a result, individuals boost their understanding of science and feel empowered by having opportunities to exert influence. Disinformation in the public arena is decreased, and the routes of access to trustworthy sources of information are strengthened. Policy-makers play important role in ensuring and facilitating open science by setting data management processes, open access legislation, developing ethical guidelines for experiments As a result, higher quality of research done with open science principles and efficient communication between stakeholders leads to better-informed decisions This figure briefly shows how three groups of stakeholders interact with each other. Healthy interactions will foster respect and overcome power dynamics. Each group should focus on empowering other groups and be aware that open science cannot exist without the others. Resources and tools for interactions are described in greater detail in Lesson 5 (and module X). Case scenarios Now let's take a look at examples of successful interactions around the world! Case Scenario #1: Trend: Public —> Policy-makers The public has many opportunities to join research projects and can play prominent roles in science. There are more than 30 ways to define Citizen Science (Haklay et al., 2021), and the principle is "active public involvement in scientific research" (Irwin, 2018). Citizen Science contributes to policy making at various stages of the policy cycle, including policy preparation, formulation, implementation, monitoring, and evaluation Scade et al (2021). That is to say, citizens are capable of setting trends and informing the directions in policy making. In 2015, the United Nations adopted the 2030 Agenda for Sustainable Development for peace and prosperity for people and the planet, now and into the future (United Nations, 2021). This agenda has 17 specific goals that require a large amount of data. Citizens have been contributing by providing the water and air quality, marine litter, biodiversity, health, and gender issues data (Fritz et al, 2019), and Scade (2021) describe this as " a source of information for policy making." This is a powerful example of citizens influencing global policy trends. Case Scenario #2: Officialize: Policy-makers—> Researchers/Public Policy-makers can implement new regulations for both researchers and the public. Bothwell and Smith (2017) reported that policy can shape knowledge. For example, policies such as dispersion of research funding (i.e. which science disciplines including Citizen Science receive the most funding), and data management plans for the public can impact the amount of knowledge produced. Most importantly, policy-makers are mindful that researchers and citizen scientists conduct science projects safely and ethically. National Institute of Health (2022) states that policy sometimes sets the rules of the road for conducting research, helping ensure that scientific investigations are carried out safely, securely, adhering to the highest standards of research integrity, and in a way that addresses evolving ethical concerns. We can find these ethical policies, for example, NIH Guidelines for Human Stem Cell Research. Some countries have legislation requiring research to be published openly, such as Spain's open access legislature. Policies on open access for European countries are monitored and reported by corresponding OpenAire National Open Access Desks. Case Scenario #3: Participate: Public —>Researchers Currently, NASA has 28 Citizen Science projects that are open to people around the world (NASA, 2022). According to NASA Citizen Science policy, Citizen Science is defined as a form of open collaboration in which individuals or organizations participate voluntarily in the scientific process in various ways. The projects vary from Earth and planetary science to biological science such as researching meteorites, mosquitos, and the surface of Mars. One of the evaluation criteria for NASA Citizen Science is; two-way communication between volunteers and NASA scientists and including diverse citizen scientists, with scientists giving feedback to and receiving feedback from the volunteers (NASA SMD Policy Document SPD-33, 2018). Also NASA creates opportunities for citizen scientists to be co-authors for publications and 191 NASA Citizen Scientists joined scientific publications since 2011 (NASA, 2022). In addition to citizen science, there is an emerging concept called community science and co creation. Community science refers to science projects that honor community priorities. They can be initiated by a science practitioner or a community member, but they must become a collaborative endeavor (ASTC, 2021). Co-creation in science refers to the collaboration between a variety of actors (people from different societal roles) actively joining forces to tackle jointly defined challenges (Stier and Smit, 2021). We can also state that community science, which prioritizes community needs, succeeds through efforts of co-creation. Charles et al (2020) introduced a successful case of community science. One example is protecting one of the remote islands in Canada that is facing the threats of sea level changes (e.g. salt water intrusion to groundwater and losing archaeological sites). As a result of community science and co-creation through public, universities, and policy makers, now climate-related mapping and visualization techniques for vulnerability assessments are available for use within the community. This provides opportunity for all the residents to explore adaptation options to ongoing sea level changes. The community was also able to work with archaeologists on preservation initiatives. Case Scenario #4: Share: Researchers —>Policy-makers/Public About 2,000 researchers work together to create a report for the Intergovernmental Panel on Climate Change on the current situation, which is a technical report that most people would have trouble understanding (Woolston, 2016). Some climate researchers break down their results to explain to policy-makers and citizens. Policy makers can utilize the results to officialize the restriction of CO2 emission level (e.g. Paris Agreement) and the public can be aware about what they can do in their daily lives to achieve the CO2 emission goal. This shows that each group is playing a significant role in addressing the climate science project, which is considered as one of the critical issues that our generation is facing. How diverse stakeholders are included in open science: Stakeholders are incredibly diverse in terms of culture, communication, and ability. To make science truly open, we must ensure that open science is accessible to everyone, so that we can all fully participate and benefit from the work. The best way to include stakeholders is to remove existing barriers and design for inclusion. Creating a more inclusive environment will both increase the amount of people who feel welcomed to contribute back to your research and will broaden the scope of people that can comprehend and interact with the products of the research. Small actions towards conforming to accessibility and diversity guidelines will go a long way towards making your work truly open to all, maximize the visibility and impact of research.. Let's look at some factors and potential barriers for participation in the open science, with possible solutions: Socioeconomic status: Instabilities in the electric, electronic and internet access (e.g. load-shedding, internet speed, electronic device performance) Possible solution(s): open science materials and communication channels should require less resources whenever possible Neurodivergence: Diversity of neural architecture leads to different learning and socialization styles Possible solution(s): employ multimodal communication strategies using different visual and audio outputs, varied pace of events and conversations Disability/impairments Sensory - e.g. colorblind, blind, deaf, auditory and/or visual processing conditions Physical - e.g. conditions that affect energy levels, neuromuscular coordination conditions Mental - conditions that affect mental health (e.g. depression, schizophrenia, etc) Possible solution(s): employ multimodal strategies and universal design to provide proactive accommodations for as many as possible - captions, transcripts, colorblind-friendly palette, document formatting that are compatible with screen readers, normalizing flexible work schedules and rolling deadlines with collaboration Intersecting Identities and intersectionality Epistemic oppression - e.g. dominance of English as the international language for all science. Non-native English speakers are disadvantaged by default. Possible solution(s): Proactive translation of open science results/communications in other languages Microaggressions/macroaggressions: use of words with negative connotations towards individuals and groups and negative behavior/ostracization Possible solution(s): Employ language and communication with neutral connotations that do not use pejorative terms or vilify a group (example) in biology, we use males to identify the parent with testes and the female with ovaries; should change language to "parents with testes/ovaries" etc) Gender Inclusive Biology for more detail Caution: Full participation in open science requires respect of an individual's identity, autonomy, and lived experiences. Microaggressions, macroaggressions, and epistemic oppression are identity barriers to open science. This list is not comprehensive, but is meant to be a starting point in preparing your work in open science for diverse stakeholders. Activity/exercise Now let's practice by looking at some typical case scenarios and solutions, reflecting on things you could do for inclusion: Case Scenario #1: Accessible figures and writing You have finished your project and are busy typing your paper to submit to an open science preprint journal. In your paper, you have several figures that use multiple colors at once - red, green, and blue. In addition, you have formatted your paper to use a serif font at size 10. You want to make sure that your paper is easily readable for everyone. What are some things you can do? Colorblind people have high difficulty with red, green, and blue colors. You can check your figures by running a color blind simulator, e.g. open source RGBind. Consider using colorblind-friendly palettes with colors such as green, magenta, and others. Avoid using color hues to convey information if at all possible. Legally blind and dyslexic people have difficulty with font size and font types. Consider using a font size of 12 or higher, and use a 'Sans-Serif font' such as Arial or Verdana to assist people with dyslexia in reading your manuscript. Bonus question: What should you do if a journal insists on using a font size and font type that is inaccessible to some people? Case Scenario #2: Organizing an inclusive physical event You are the head organizer for an open source code hackathon for your organization. Your boss initially suggests using the large seminar room with one projector and screen that is hard to see from the back of the room. When starting the hackathon, you find out that a couple of attendees are deaf and a couple of other attendees have visual difficulties. What are some quick things you could do to help them fully participate in the hackathon? If doing a presentation on Powerpoint, you can turn on 'Always use subtitles' for live transcription. Check if your font size on your presentation is large enough to comfortably see at the back of the room. If possible, consider simulcasting the presentation on Zoom or other virtual platform with captions/transcription. Use text for communicating with deaf attendees. Case Scenario #3: Organizing an inclusive virtual meeting and preparing in advance You are organizing a virtual open science meeting with established and prospective members from different countries. You are unsure of what the prospective members need in order to participate fully, and no one emailed you to let you know about accommodations they need. What should you do? Being proactive with small things you can do ahead of time by implementing some of the accommodations before the meeting (see possible solutions to barriers that we have just considered). While it is difficult to preconceive every possible accommodation that you might need to provide for your members, if you communicate your willingness to do everything you can to help members thrive, you are doing incredibly important work to not only recruit prospective members to open science, but also to retain them. Bonus tip: Subtitles and closed captioning are not only for deaf/hard-of-hearing people, they are also very beneficial for non-native English speakers to understand the conversation fully. Consider using a third-party app such as otter.ai for accurate closed captioning and simultaneous transcripts that can be saved for members to read through. What are some other accommodations that could be useful for everyone in general? Summary In the first part of this lesson, we learned about the types of stakeholders and how they can interact to empower each other. Successful examples were introduced, and you can reflect and analyze how to develop these interactions in your science projects. These arrangements may initially take time, but the outcome is essential to advance science, and is also rewarding. In the second part of the lesson, we studied how diverse stakeholders can be included in open science with case scenarios designing for inclusion. Taking measures to maximize diversity, inclusion, and accessibility of your science project will enrich the project, boost its visibility and engagement of participants. Healthy interactions among stakeholders with diverse members creates the strength of science projects and rewarding results, and a diverse team drives innovation to success. Remember that what you learned here is not an optional choice but an integral part of responsible Open Science. To learn more about joining, contributing to, and creating your own communities, consider visiting the Tools module. ``` Questions/Reflection: ``` What steps can you take to make these open science resources more inclusive? Written resources and images Conferences - virtual, physical, or hybrid Communication with the general public and policy makers should not be something that researchers only do when they have spare time, after the research is done and published. It should be treated as a critical part of a science project, to certain extent at all stages of development Explain multiple possible communication channels and strategies for researchers, and why each is important . ``` --- ### ### Lesson 4: WHERE: Impact of Open Science on academia, communities and society as a whole: Where open science happens. >>>>> gd2md-html alert: Long single-cell table. Check to make sure this is meant to be a code block. (<a href="#">Back to top</a>)(<a href="#gdcalert6">Next alert</a>) >>>>> ``` Introduction We have so far explored the fundamental parts of what Open Science is: why to pursue it and who the stakeholders of open research are. Where you are in the world when performing open science can have an impact on how you perform it, too. Laws across the world vary, and the advantage of open science means people from around the world can participate, co-create, and consume content together. This can affect your work from social and legal perspectives, and may present technical challenges as well. Legal frameworks that affect responsible Open Science Open Science promises to make research work more accessible, all-encompassing, participatory, understandable and re-usable for wider audiences. Keep in mind, making the process open does not in itself result in wide participation unless it's partnered with sufficient financial resources, technological advancements, knowledge and skills. It's important that all these are available across regions, institutions and socio-demographics (review by Hellauer et al. 2022) Data protection, privacy, and data sovereignty Caution: To perform open science responsibly, it is important to consider not only what you should share, but also what not to share. Individuals may have a right to privacy in their communications, for medical records, and for their physical locations. Similarly, certain countries, communities, and especially Indigenous peoples may historically have been exploited, and may wish to retain more rights over their knowledge to protect from further exploitation. Globally, there are laws around the world that may cover some of these issues, but not all countries and regions have equal levels of protection, and some have none at all. We share some case studies: European case: General Data Protection regulation There are protective laws and legal frameworks in certain places around the globe that affect open science. European researchers have to abide by the General Data Protection regulation (GDPR) while making a data sharing statement stating the non-availability of data sharing. This hinders sharing particular data. Here, the scientific society should come forward to allow responsible Open Science data sharing possibilities in the global scientific space (Giske Ursin & Heidi Beate Bentzen, 2021) South African case: Protection of Personal Information Act (POPI Act) and Open Science The POPI Act No. 4 of 2013 is regulation by the government of South Africa to safeguard the personal information of South African citizens, like the General Data Protection Regulation (GDPR) in Europe. The regulation states that if one is obtaining personal information of South African citizens through phones, focus groups, interviews, containing identifiers such as names, contact information then you have to be POPI Act compliant. In the research context, one needs to make sure that if the personal identifiers are collected then they must not be shared with third parties and stored securely in an access-controlled location to prevent a data breach. The act doesn't impede open data sharing, but personal identifiers should be removed from shared datasets. The POPI act affects the research process, in a way to make sure that storing of data of only de-identified datasets on cloud storage & onsite data storage is strictly controlled to specific designated individuals to ensure data safety (POPIA Code of Conduct for Research, 2021). United States case: In the United States, there is no federal-level legislation similar to POPI or GDPR, but there are some state-level laws, such as the California Privacy Rights Act, and the Virginia Consumer Data Protection Act. Exercise: Check what laws, if any, apply in your state. Summary: Working in a global society with varied data protection laws Given the broad variation of data protection laws around the world, it may seem tricky to navigate. By practicing responsible Open Science, however, our response can get a little bit clearer. We can consider relevant legislation (if any) to be a bare minimum, and instead ensure that we are involving relevant stakeholders, as discussed in lesson 4, and listening to their needs respectfully, even if it means we are more cautious than local legislation may require. Whose laws apply to my community? Social, cultural, and legal norms will vary from country to country, and international communities. Avoiding culture clashes can be made more manageable by setting out explicit cultural norms for your community, such as may be specified in a code of conduct, which we discussed in lesson one of this module. Try to avoid assumptions that tie to a specific physical location or culture. Some examples why this is important: Laws are not uniform. If activity X is legal to do in one country, but not another, a code of conduct which says "obey the law" becomes impossible to interpret fairly or to enforce. Hosting a conference in a country that doesn't have strong human rights records might result in someone breaking the law by being LGBTQIA+, or by not wearing religious garb. "We plan to release this in the summer" might be clear if you're all in the same country, but if your collaboration is spread across the northern and southern hemisphere, is summer in the middle of the year or the end of the year? Consider using a month name instead - "we plan to release this by March" is unambiguous. Equity and Open Science Many countries in Asia, Africa and Latin America face many challenges, including lack of funding, inadequate access to literature and poor infrastructure. Across these regions, young scientists are working to build practices for open science from bottom-up. The aim is that scientific communities will incorporate these principles as they grow but these communities' needs differ from those that are part of mature research systems. The reasons for falling behind are lack of funding, poor infrastructure,inadequate access to research resources. There are government policies, which want greater productivity at the expense of quality. The open science collaborations can bridge the gap for developing countries by providing new ways and provide researchers access that might be currently out of reach (Onie, S. 2020). PULL-OUT BOX: Equitable terminology: what words should we use? When talking about equity from a global perspective, it can be very hard to choose appropriate language, and historically many phrases have come and gone as we learn more equitable ways to communicate. Common phrases you may see include "Higher Income Country" and "Lower or Middle Income Country". These are terms defined by the World Bank. Some people prefer to use "Global North" when referring to more privileged / high income countries, and "Global South" for lower income / more exploited and marginalized countries - but some "Global South" countries are in the northern hemisphere, and vice versa! Other times, people use "minority" and "majority", but again sometimes the phrase "minority" might be used for a populace that is not actually a minority! An older phrase is "first world country" or "third world country". Many of these terms also have accidental or intentional negative connotations. For this module, we aim to use the phrases "marginalized" and "privileged" when referring to the inequitable distributions of resources and power amongst humanity. The Global North have ascendency over authorship and synergies in research networks, which margins out the Global South (Cash-Gibson L et al 2018). In richer regions, a compulsion for the goal of excellence nurtures cumulative benefit in funding allocation for the highest funded institutions (Noble P et al) Across many countries, very few women have higher positions, senior positions are given at a later age, given less grant funding and few have high-impact publications (Gesiarz F et al 2020) (Brown JVE et al 2020 ) These are the impartialities, which are the societal imbalances (Zuckerman H. (1988). The above stated societal imbalances, which Open Science is focused to minimize in order to elevate the underrepresented societies, groups and create avenues for Global South countries to come forward & contribute to the global science community. Prainsack & Lionello (2018) stated that open science is a political assignment greater than its technological part. The Open Science policy in Europe is shifting across nations, institutions & funding organizations. (Sveinsdottir T et al 2020) . The emphasis on policies drive the incentive/reward structures and resource allocation and later helps in establishing strategies. Open Science started as a bottom-up approach by the researchers but has gone to the top-end level making it to the national and institutional policies setting wider goals like economic growth. The European Commission favors Open Science but in 2016 EU publication, the concern of Open Science perceived potential is being given that greater importance for fostering Europe's competitive advantage in global markets (link to EU publication, 2016) Open Science positions to cover literature in languages other than English, supporting the value of 📖bibliodiversity📖. We see a diverse set of communities in organizations working for Open Science data, software, tools, resources together as multilingual teams' covering different languages of the world. Research indicates that there is a demand for regionally focused titles, in regional languages (Snijder 2022).. A global perspective on open science UNESCO on Open Science Infrastructure UNESCO's recommendation on Open Science states the potential of open science is in minimizing the present inequalities in Science, Technology and Innovation and pace towards SDGs 2030 implementation agenda, specifically in Africa, least developed countries, small island developing states and landlocked developing countries. Open Science infrastructures are shared infrastructures (referred as virtual/physical, knowledge-based resources such as journals, collections, and open access publication platforms, archives, repositories, scientific data, present research informations systems, sets of instruments, open bibliometrics, scientometrics systems for assessing & analyzing scientific areas, open computational & data manipulation service infrastructures, multidisciplinary data analysis & digital infrastructures) where open science happens and serves the needs of diverse communities. Please see UNESCO Recommendation on Open Science UNESCO on Open Science policies clearly recommends monitoring Open Science through combining qualitative and quantitative methods to assess the efficacy and efficiency of Open Science as per the member states' particular conditions, constitutional structures and constitutional provisions. Also, gathering & communicating progress, good practice, research work & innovation in open science and its outcomes with support of UNESCO and diverse stakeholders approach. Organisation for Economic Co-operation and Development (OECD) and Open Science The OECD's recommendation regarding research data from public funding helped gain collaboration and global sharing of data as a policy priority, with the objective of making the global science system more effective and seamless. There has been progression in a number of OECD member states and partner economics, with 58 countries successfully delineating their policies for open data & research publications. For IT infrastructure, academic institutions and data repositories, international networks have been established in the form of repository networks such as OpenAIRE. "Science clouds" - national and international computational resources - are being initiated such as European Open Science Cloud, the Australian cloud NECTAR, the National Research Data Infrastructure in Germany, the National Institute of Health Data Commons in the USA & Research Center for Open Science and Data Platform in Japan. ``` Questions/Reflection: ``` What strengths do marginalized communities bring to open science? What challenges may they face compared to privileged communities? Name at least one data privacy law, and describe ways you can keep personal data safe. Do all countries have data privacy laws? Bonus: You're working on an open science consortium that gathers data in the Netherlands, Kenya, and India. You plan to use servers in the EU to store your data. What concerns should you take into account? ``` --- ### ### Lesson 5: HOW: >>>>> gd2md-html alert: undefined internal link (link text: "Open Science resources & tools: How to get started"). Did you generate a TOC? (<a href="#">Back to top</a>)(<a href="#gdcalert7">Next alert</a>) >>>>> [Open Science resources & tools: How to get started](#heading=h.yeglp8w955sj) in responsible Open Science (doing open science responsibly) <table> <tr> <td> <h4>Introduction</h4> Previous lessons have shown the importance and benefits of open science, presented some key stakeholders involved, and discussed the barriers to participation and ways to overcome them. This lesson will guide you in how to start infusing responsible Open Science in your own work, which might be independent, or could be in a research group or lab. <h5>Not an afterthought - plan for open science into the design</h5> Practicing responsible Open Science requires organizing your work and research, and your team, if you have one, around open science and planning for it from the inception, even designing the project with open science in mind. There are many resources and tools that make these easy, and indeed doing so will improve efficiency and the value and impact of your work, and help you focus on your research itself. We’ll provide a brief overview in this lesson, but you may wish to explore the later modules in this course too, which cover 🔗 Open Data, Open Results, Open Tools, and Open Software 🔗. Additional resources, and knowledge, may be available at your institution, including in your department or library or among your colleagues. An additional resource is a recent report from the U.S. National Academies “<a href="https://nap.nationalacademies.org/catalog/25116/open-science-by-design-realizing-a-vision-for-21st-century">Open Science by Design</a>.” It is important to discuss responsible Open Science with your research team, lab, group or partners regularly. Much of responsible Open Science may seem to be related to outputs – such as data, software, and publications – but preparing and organizing work for these in advance is critical. It would be hard or impossible to follow leading practices for these at the end of research, in the “afterthought” mode. responsible Open Science is both a mindset and culture. Planning for outputs in advance includes: speaking about it and organizing with your research team; deciding which tools to use; thinking about authorship and credit; engaging with relevant stakeholders and research partners, for example, industry, around open science; identifying repositories for software and data; highlighting these approaches in your grant; and much more. <h4>Perks of digital and internet age for responsible Open Science: </h4> The internet has made it very easy to share digital work. The popularization of Open Source computer code and the rise of Open Science has resulted in many outlets for public and free hosting of research and data.One key to open science, and why it is so empowering for 21st century science, is that we can now connect all the participants, stakeholders, and outputs of a research result together so that they are easy to discover. Here we present a non-exhaustive list of digital platforms and tools used with for open science: <ul> <li>Digital Persistent identifiers - for objects and researchers (such as doi and ORCID) <li><a href="https://pkp.sfu.ca/ojs/">Open Journal System</a>: open source software for managing & publishing scholarly journals <li>Electronic notebooks such as <a href="https://jupyter.org/">Jupyter</a> and <a href="https://rmarkdown.rstudio.com/">R Markdown</a> <li>Data repositories: genetic sequence database <a href="https://www.ncbi.nlm.nih.gov/genbank/">Genbank</a>, protein data bank (<a href="https://www.rcsb.org/">PDB</a>), Dataverse, figshare, Zenodo and for wide search use <a href="https://www.re3data.org/">https://www.re3data.org/</a> and/or <a href="https://datacite.org/">https://datacite.org/</a> <li>Softwares/Codes: Zenodo used with Github / mybinder <li>Materials: Addgene (for molecular biology) <li>Reference management tools: Zotero, Mendeley <li>Academic Social networks: Academia.edu, ResearchGate <li>Peer Review: Publons, PreView <li>Project management: Open Science framework <li>Github as a platform for collaborative work on training materials etc A variety of tools are emerging to help manage open science workflows, and to support global collaboration. These include spaces for project management, such as the Open Science Framework from <a href="https://www.cos.io/">Center for Open Science, electronic</a> notebooks which help projects organize data, software, and content together; online platforms for creating manuscripts, etc. More information about the open science collaboration and management tools are described in the 🔗Open Tools module🔗. Now let’s move to the tools and procedures to ensure credit and attribution for our work, and allow its use and reuse in new, powerful ways, using the internet. <h4>Digital persistent identifiers - for objects and researchers</h4> A key to the 📖interoperability📖 is that each piece is assigned a “📖persistent identifier📖” and “📖metadata📖” that provides a secure path and basic information about it in such a way that they can be linked automatically (machine-readable). How many times have you gone to an old link, only to find the page is no longer there? A persistent identifier is powerful because it is designed to point to the Web resource even if, or when, the URL or domain changes. One very common type of persistent identifier is a “📖digital object identifier” (DOI)📖 that is usually assigned to a digital object (e.g. document) by publishers, preprint servers, data and software repositories. This has allowed automated linking of references across publications, including to citations after a publication. Case scenarios: <ul> <li>A researcher writes a script in R that they use to analyze their results and produce a bar chart. They can upload their R code to a repository, and get a DOI for their script, so others can peer-review the code if they wish. <li>A member of the public attends a conference online and shares a digital poster and a short talk about their work as a citizen scientist. They deposit their poster and talk slides on to Zenodo, and can share the slides and poster using the DOI URL and receive credit for it. <li>A consortium member collaboratively authors a paper summarizing the results of a workshop they attended, alongside other workshop attendees. The journal they publish in automatically assigns a DOI to the paper. <h5>ORCID: A permanent unique identifier for you, as a scientific author</h5> Researchers and authors also have a digital identifier in this system: The Open Researcher and Contributor Identifier or ORCID. Thus a first step to enabling responsible Open Science is to sign up for your identifier at <a href="https://ORCID.org">https://ORCID.org</a>. This identifier will be included in your research outputs and work so that they can be linked uniquely to you (this can also happen automatically). You control your information on ORCID and what is public or private. Your ORCID can also be a way to get credit and recognition for reviews, awards, and more. Many funding agencies now integrate fully with ORCID, for example, for preparing grants and reference lists. Other identifiers that are regularly used include those for funding agencies–which along with the grant ID provide a connecting link back to their repositories, institutions, 📖samples📖, open reviews, and even 📖annotations on web pages📖. Identifiers for 📖research instruments📖, 📖reagents📖, and materials are under development and implementation too. In most cases, the identifiers will not be managed or assigned by you. Publishers and data repositories may ask you and your co-authors to link your ORCID and provide a grant ID (if you have one!) but they will then automatically provide the digital linking and create the 📖metadata📖 record. Often, you can sign on to repositories using your ORCID, so that this is automatically linked to any work you upload. Having basic metadata - remember, metadata is documentation about your data - for each object with a persistent identifier helps 📖discoverability📖. For publications and datasets, an identifier usually includes the title, authors (with their own identifiers), grants (with identifiers), journal (with its identifier as well, the ISSN), and publication date among other information. This allows search engines to discover and index the content. For data sets, leading repositories will also help ensure that information on standards, uncertainty, and calibration are included to allow appropriate reuse. Collectively, this system allows widespread discovery and connection of the various pieces of research–even connecting open preprints and conference presentations to later versions and publications to data sets that underlie and support them. <h4>Sharing data, and software, and getting cited: Repositories you can use</h4> Thus a key part of responsible Open Science, which is enabled by this system, is that research outputs – data sets, software, publications, conference reports, etc.--should go to the respective places that best manage, curate, and host that type of output. Previously, a data set may have been included as a supplement to a paper, usually a PDF file at a publisher’s site, or not included at all (“data not shown" or “data available upon request” statements were common even a few years ago but are thankfully waning). Publishing a data set separately from your paper, at a repository that handles that type of data well (ideally a popular “📖domain repository📖”), allows others to cite your data separately, with its own metadata and authorship and expert curation of that data. Some also allow data that have appropriate restrictions on access (such as personal medical data) to be hosted in a secure way. This allows separate credit and authorship (if appropriate) for data or software products. A publication or research project may, and often will, have multiple data sets across several leading repositories. In general, domain repositories are preferred over a general repository for data, because of the 📖expert curation📖 and better metadata they can provide, but not all disciplines or types of data have appropriate repositories. In this case general repositories can be used. In some cases, you may create and deposit data in a repository throughout a project; in other cases the natural time to “publish” the data is when a paper is submitted to a journal. See the 🔗Open data module🔗 for more information on sharing your data appropriately. . Open software is usually developed in a collaborative workspace such as GitHub. Github works with a general repository, Zenodo, to enable software versions to be assigned an identifier and metadata. Sharing data, codes and software is a key for ensuring reproducibility of findings, improvement of code and software, for enabling other researchers to easily re-use , extend and cite that work (<a href="https://www.biorxiv.org/content/10.1101/039354v2">Gorgolewski & Poldrack, 2016</a>). Sharing the data & materials is also a signal of valuing transparency and trust in their own research, boosts authors' visibility and recognition <a href="https://elifesciences.org/articles/16800">(McKiernan et al., 2016)</a>. See the 🔗Open source module🔗 for more information on sharing your code and software appropriately. Collectively, this set of identifiers, metadata, and infrastructure helps enable content and especially research data to be “findable, accessible, interoperable, and reusable” or <a href="https://www.go-fair.org/fair-principles/">FAIR</a>. This is a key concept and part of responsible Open Science. For researchers it means directing research outputs to their best open science home and planning for this throughout the research process. For all these reasons, it is best to think about how to share data and software supporting a publication before submission. More about FAIR principles can be found in the 🔗X module🔗, and now we will consider some foundational principles on licensing the content for reuse. As a general rule, when you create something - a blog post, a scientific paper, a drawing, a data set, computer code, or any other ‘creative’ work - you automatically own the copyright for that work yourself. This means that others aren’t allowed to re-use it without your permission, even if it’s freely available on the internet. As an open scientist, you can use a 📖license📖 to grant others permission to re-use your work, and even specify conditions - perhaps you always want others to credit your work, or perhaps you don’t want your work to be used commercially. Caution: When you perform work for someone else, as an employee, contractor, volunteer, or a student, your contract may stipulate that the copyright for that work belongs to the institute you are working for. Before assigning a license to your work, check that you have the right to do so. Your employer, institution’s intellectual property office, and your funder may all have specific expectations around how you share your work and what license you use. Distributing content to the best open science home also allows each output to have the right license that allows access and reuse. Usually you would include the type of license in the metadata. When you publish a preprint or publication, or deposit a dataset, or software version at a repository, you will usually be asked about the correct license to assign to that content. Usually a repository will recommend or require a specific license to enable broad reuse. The basic standard is that leading licenses support reuse generally with attribution (citation) so that the creators of the content are recognized. Citations are supported by leading publishers. Here we list general guide on the best licenses for published content, data, and software: <ul> <li>Written content of any kind, papers, posters, slides, images, audio files, videos, other creative works <ul> <li><a href="https://creativecommons.org/">Creative Commons licenses</a> are designed to allow re-use of these types of content. Authors can choose to require credit for their work (CC-BY attribution), allow or disallow commercial use and/or derivative works, and to require <a href="https://en.wikipedia.org/wiki/Share-alike">reciprocal sharing</a> of works. 🔗Open Results Module for more information🔗 </li> </ul> <li>Data - including spreadsheets/csv/text files with experiment results, videos/audio files/images created from a study, databases of computationally processed data. <ul> <li><a href="https://creativecommons.org/publicdomain/zero/1.0/">Creative Commons Public Domain (CC0) licenses </a>are often best for data. Whilst you may be tempted to use a creative commons attribution license (CC-BY), this can make it difficult for people who wish to reuse or integrate different data sources in the future. Visit the 🔗Open Data Module for more information🔗. </li> </ul> <li>Computer code, such as scripts written in R, Python, Matlab, SPSS. <ul> <li><a href="https://opensource.org/licenses">The Open Source Initiative</a> has a set of licenses designed specifically for code projects, that covers both open distribution of the code itself, as well as executable versions of the program that non-programmers can run. Visit the 🔗Open Source Module for more information🔗 </li> </ul> <li>Other items: Whilst this is beyond the scope of the module, this list is not exhaustive. Other types of work may require different license types. For example, what license would you use for an open hardware drone design, a 3d-printed microscope kit, or a reagent used in a laboratory? These items may have different constraints and needs. The overview of the type of creative common licenses is presented in the figure. (( Place for visual )) >>>>> gd2md-html alert: inline image link here (to images/image3.jpg). Store image on your image server and adjust path/filename/extension if necessary. (<a href="#">Back to top</a>)(<a href="#gdcalert8">Next alert</a>) >>>>> <img src="images/image3.jpg" width="" alt="alt_text" title="image_tooltip"> Caution: As a general rule, if an item does not include a license for reuse, it’s illegal to reuse even if you can see the work online. Licenses are designed to take into account the legal ins-and-outs that each type of work can encounter. Try not to use one license type for a different output - Creative Commons specifically advises <a href="https://creativecommons.org/faq/#can-i-apply-a-creative-commons-license-to-software">not to use their licenses for computer code</a>, for example. <h4>Making your work useful to others: </h4> <h5>Sharing and publishing your manuscript:</h5> <h6>Public repository/Preprints:</h6> Sharing drafts of research as preprints can improve citations and help establish or provide credit and a reference months before formal publication in the journals (<a href="https://elifesciences.org/articles/16800">McKiernan et al 2016</a>) A manuscript posted by author(s) to a repository for facilitating open sharing of early work without any limitations to access is 📖Preprint📖 (<a href="https://doi.org/10.3998/mpub.12412508">Puebla et al 2022</a>). Basic screening is carried out to the manuscript, which is usually posted on the preprint server within a few days of submission without peer review and is freely accessible online. More than 1200 journals now allow posting of preprints, and some connect directly to deposit submitted manuscripts directly (see directory here: <a href="https://v2.sherpa.ac.uk/romeo/">https://v2.sherpa.ac.uk/romeo/</a>) or allow transfer from the server to the journal. Many funding agencies now allow citations of preprints in grants. Many preprint repositories are field-specific; see a directory here: <a href="https://asapbio.org/preprint-servers">https://asapbio.org/preprint-servers</a>. Many also will link to the published version of the manuscript once it is available. In addition, many institutions have open sharing repositories, and mandates to share author-versions of published manuscripts. Many funders also have repositories for sharing manuscripts after publication or a means to connect to manuscripts on publisher platforms. Check with your institution or funder, and journal publisher for requirements. Some preprint repositories also accept conference presentations (e.g. posters and slide decks for talks). <h6>Publishing Open Science and Open Access</h6> When you publish your work in peer-reviewed journals, traditional publishing models may result in papers that are not openly available for anyone to access, and instead may require a