Lesson on OpenRefine for social scientists. A part of the data workflow is preparing the data for analysis. Some of this involves data cleaning, where errors in the data are identifed and corrected or formatting made consistent. This step must be taken with the same care and attention to reproducibility as the analysis. OpenRefine (formerly Google Refine) is a powerful free and open source tool for working with messy data: cleaning it and transforming it from one format into another. This lesson will teach you to use OpenRefine to effectively clean and format data and automatically track any changes that you make. Many people comment that this tool saves them literally months of work trying to make these edits by hand.

Topics covered:

Understanding reproducible research
Setting up a reproducible project
Understanding power
Preregistering your study
Keeping track of things
Containing bias
Sharing your work

Open science reduces waste and accelerates the discovery of knowledge, solutions, and cures for the world's most pressing needs. Shifting research culture toward greater openness, transparency, and reproducibility is challenging, but there are incremental steps at every stage of the research lifecycle that can improve rigor and reduce waste. Visit cos.io to learn more.

The Open Research Toolkit was created by Christopher Eaker during Faculty Development Leave, Fall 2021. While this toolkit was designed for librarians for learning open research concepts and skills and teaching them at their institutions, it would be useful for anyone interested in learning more about open research. Any questions related to this content can be directed to the author.

The ORT YouTube Channel is found here: http://doi.org/10.7290/ORT_Videos

The Open Research Toolkit is an Open Educational Resource, and is available under Creative Commons Attribution 4.0 International (CC BY 4.0). You may re-use and copy information from this toolkit with attribution. In addition, some of the materials referenced in this toolkit (e.g. some materials linked to and created by others) might be copyright protected; that will be indicated as best as possible, but no guarantees are made as to accuracy of that information. The user should check restrictions of any material prior to reusing it.

About This Document: This manual was assembled and is being updated by Professor Benjamin Le (@benjaminle), who is on the faculty in the Department of Psychology at Haverford College. The primary goal of this text is to provide guidance to his senior thesis students on how to conduct research in his lab by working within general principles that promote research transparency using the specific open science practices described here. While it is aimed at undergraduate psychology students, hopefully it will be of use to other faculty/researchers/students who are interested in adopting open science practices in their labs.

“Open Science” has become a buzzword in academic circles. However, exactly what it means, why you should care about it, and – most importantly – how it can be put into practice is often not very clear to researchers. In this session of the SSDL, we will provide a brief tour d'horizon of Open Science in which we touch on all of these issues and by which we hope to equip you with a basic understanding of Open Science and a practical tool kit to help you make your research more open to other researchers and the larger interested public. Throughout the presentation, we will focus on giving you an overview of tools and services that can help you open up your research workflow and your publications, all the way from enhancing the reproducibility of your research and making it more collaborative to finding outlets which make the results of your work accessible to everyone. Absolutely no prior experience with open science is required to participate in this talk which should lead into an open conversation among us as a community about the best practices we can and should follow for a more open social science.

There is a vast body of helpful tools that can be used in order to foster Open Science practices. For reasons of clarity, this toolbox aims at providing only a selection of links to these resources and tools. Our goal is to give a short overview on possibilities of how to enhance your Open Science practices without consuming too much of your time.

A group of fourteen authors came together in February 2018 at the TIB (German National Library of Science and Technology) in Hannover to create an open, living handbook on Open Science training. High-quality trainings are fundamental when aiming at a cultural change towards the implementation of Open Science principles. Teaching resources provide great support for Open Science instructors and trainers. The Open Science training handbook will be a key resource and a first step towards developing Open Access and Open Science curricula and andragogies. Supporting and connecting an emerging Open Science community that wishes to pass on their knowledge as multipliers, the handbook will enrich training activities and unlock the community’s full potential.

In this first release of the Open Science Training Handbook, some initial feedback from the community is already included.

Open Science, the movement to make scientific products and processes accessible to and reusable by all, is about culture and knowledge as much as it is about technologies and services. Convincing researchers of the benefits of changing their practices, and equipping them with the skills and knowledge needed to do so, is hence an important task.This book offers guidance and resources for Open Science instructors and trainers, as well as anyone interested in improving levels of transparency and participation in research practices. Supporting and connecting an emerging Open Science community that wishes to pass on its knowledge, the handbook suggests training activities that can be adapted to various settings and target audiences. The book equips trainers with methods, instructions, exemplary training outlines and inspiration for their own Open Science trainings. It provides Open Science advocates across the globe with practical know-how to deliver Open Science principles to researchers and support staff. What works, what doesn’t? How can you make the most of limited resources? Here you will find a wealth of resources to help you build your own training events.

Open Science is a collection of actions designed to make scientific processes more transparent and results more accessible. Its goal is to build a more replicable and robust science; it does so using new technologies, altering incentives, and changing attitudes. The current movement towards open science was spurred, in part, by a recent “series of unfortunate events” within psychology and other sciences. These events include the large number of studies that have failed to replicate and the prevalence of common research and publication procedures that could explain why. Many journals and funding agencies now encourage, require, or reward some open science practices, including pre-registration, providing full materials, posting data, distinguishing between exploratory and confirmatory analyses, and running replication studies. Individuals can practice and encourage open science in their many roles as researchers, authors, reviewers, editors, teachers, and members of hiring, tenure, promotion, and awards committees. A plethora of resources are available to help scientists, and science, achieve these goals.

Note: This webinar was presented in Spanish. The slides presented during this webinar can be found here:https://osf.io/6qnse/ The slides presented during this seminar can be found here: https://osf.io/6qnse/ Este seminario web se centrará en el estado de la ciencia abierta en América Latina, desde los esfuerzos de los investigadores individuales para abrir sus flujos de trabajo, herramientas para ayudar a los investigadores a ser abiertos y nuevas redes e iniciativas prometedoras en ciencia abierta. Ricardo Hartley (@ametodico) es profesor de metodología de la investigación de la Universidad Central de Chile, investigador en biología de la reproducción y en comunicación - valoración del conocimiento. Organizador de las OpenCon Santiago 2016 y 2017 y embajador COS. Erin McKiernan es profesora del Departamento de Física, Programa de Física Biomédica de la Universidad Nacional Autónoma de México. También es la fundadora del Why Open Research? proyecto, un sitio educativo para que los investigadores aprendan cómo compartir su trabajo, financiado en parte por la Fundación Shuttleworth. Fernan Federici Noe es profesor asistente e investigador de la Universidad Católica de Chile y fellow internacional del OpenPlant Synthetic Biology Center, University of Cambridge. Fernan es miembro del Global For Open Science Hardware (GOSH) y TECNOx (www.tecnox.org).

This paper investigates the conceptual relationship between openness and reproducibility using a model-centric approach, heavily informed by probability theory and statistics. We first clarify the concepts of reliability, auditability, replicability, and reproducibility–each of which denotes a potential scientific objective. Then we advance a conceptual analysis to delineate the relationship between open scientific practices and these objectives. Using the notion of an idealized experiment, we identify which components of an experiment need to be reported and which need to be repeated to achieve the relevant objective. The model-centric framework we propose aims to contribute precision and clarity to the discussions surrounding the so-called reproducibility crisis.

The movement towards open science is a consequence of seemingly pervasive failures to replicate previous research. This transition comes with great benefits but also significant challenges that are likely to affect those who carry out the research, usually early career researchers (ECRs). Here, we describe key benefits, including reputational gains, increased chances of publication, and a broader increase in the reliability of research. The increased chances of publication are supported by exploratory analyses indicating null findings are substantially more likely to be published via open registered reports in comparison to more conventional methods. These benefits are balanced by challenges that we have encountered and that involve increased costs in terms of flexibility, time, and issues with the current incentive structure, all of which seem to affect ECRs acutely. Although there are major obstacles to the early adoption of open science, overall open science practices should benefit both the ECR and improve the quality of research. We review 3 benefits and 3 challenges and provide suggestions from the perspective of ECRs for moving towards open science practices, which we believe scientists and institutions at all levels would do well to consider.

In this webinar, we demonstrate the OSF tools available for contributors, labs, centers, and institutions that support stronger collaborations. The demo includes useful practices like: contributor management, the OSF wiki as an electronic lab notebook, using OSF to manage online courses and syllabi, and more. Finally, we look at how OSF Institutions can provide discovery and intelligence gathering infrastructure so that you can focus on conducting and supporting exceptional research. The Center for Open Science’s ongoing mission is to provide community and technical resources to support your commitments to rigorous, transparent research practices. Visit cos.io/institutions to learn more.

Recent literature hints that outcomes of clinical trials in medicine are selectively reported. If applicable to psychotic disorders, such bias would jeopardize the reliability of randomized clinical trials (RCTs) investigating antipsychotics and thus their extrapolation to clinical practice. We therefore comprehensively examined outcome reporting bias in RCTs of antipsychotic drugs by a systematic review of prespecified outcomes on ClinicalTrials.gov records of RCTs investigating antipsychotic drugs in schizophrenia and schizoaffective disorder between 1 January 2006 and 31 December 2013. These outcomes were compared with outcomes published in scientific journals. Our primary outcome measure was concordance between prespecified and published outcomes; secondary outcome measures included outcome modifications on ClinicalTrials.gov after trial inception and the effects of funding source and directionality of results on record adherence. Of the 48 RCTs, 85% did not fully adhere to the prespecified outcomes. Discrepancies between prespecified and published outcomes were found in 23% of RCTs for primary outcomes, whereas 81% of RCTs had at least one secondary outcome non-reported, newly introduced, or changed to a primary outcome in the respective publication. In total, 14% of primary and 44% of secondary prespecified outcomes were modified after trial initiation. Neither funding source (P=0.60) nor directionality of the RCT results (P=0.10) impacted ClinicalTrials.gov record adherence. Finally, the number of published safety endpoints (N=335) exceeded the number of prespecified safety outcomes by 5.5 fold. We conclude that RCTs investigating antipsychotic drugs suffer from substantial outcome reporting bias and offer suggestions to both monitor and limit such bias in the future.

This lesson is part of Software Carpentry workshops and teach an introduction to plotting and programming using python. This lesson is an introduction to programming in Python for people with little or no previous programming experience. It uses plotting as its motivating example, and is designed to be used in both Data Carpentry and Software Carpentry workshops. This lesson references JupyterLab, but can be taught using a regular Python interpreter as well. Please note that this lesson uses Python 3 rather than Python 2.

Among the top challenges of reproducible computational science are: (1) creation, curation, usage and publication of research software; (2) acceptance, adoption and standardization of open-science practices; (3) misalignment with academic incentive structures and institutional processes for career progression. I will address here mainly the first two, proposing a praxis of reproducible computational science.

Computational analyses are playing an increasingly central role in research. Journals, funders, and researchers are calling for published research to include associated data and code. However, many involved in research have not received training in best practices and tools for sharing code and data. This course aims to address this gap in training while also providing those who support researchers with curated best practices guidance and tools.This course is unique compared to other reproducibility courses due to its practical, step-by-step design. It is comprised of hands-on exercises to prepare research code and data for computationally reproducible publication. Although the course starts with some brief introductory information about computational reproducibility, the bulk of the course is guided work with data and code. Participants move through preparing research for reuse, organization, documentation, automation, and submitting their code and data to share. Tools that support reproducibility will be introduced (Code Ocean), but all lessons will be platform agnostic.Level: IntermediateIntended audience: The course is targeted at researchers and research support staff who are involved in the preparation and publication of research materials. Anyone with an interest in reproducible publication is welcome. The course is especially useful for those looking to learn practical steps for improving the computational reproducibility of their own research.

This video shows interested researchers how to get started on their own preregistration as part of the Preregistration Challenge. Learn how to create a new draft, find example preregistrations from different fields, respond to comments from the preregistration review team, and turn your final draft into a formal preregistration. For more information, check out https://www.cos.io/initiatives/prereg-more-information.