A two-day introduction to modern evidence-based teaching practices, built and maintained by the Carpentry community.

Psychological science is navigating an unprecedented period of introspection about the credibility and utility of its research. A number of reform initiatives aimed at increasing adoption of transparency and reproducibility-related research practices appear to have been effective in specific contexts; however, their broader, collective impact amidst a wider discussion about research credibility and reproducibility is largely unknown. In the present study, we estimated the prevalence of several transparency and reproducibility-related indicators in the psychology literature published between 2014-2017 by manually assessing these indicators in a random sample of 250 articles. Over half of the articles we examined were publicly available (154/237, 65% [95% confidence interval, 59% to 71%]). However, sharing of important research resources such as materials (26/183, 14% [10% to 19%]), study protocols (0/188, 0% [0% to 1%]), raw data (4/188, 2% [1% to 4%]), and analysis scripts (1/188, 1% [0% to 1%]) was rare. Pre-registration was also uncommon (5/188, 3% [1% to 5%]). Although many articles included a funding disclosure statement (142/228, 62% [56% to 69%]), conflict of interest disclosure statements were less common (88/228, 39% [32% to 45%]). Replication studies were rare (10/188, 5% [3% to 8%]) and few studies were included in systematic reviews (21/183, 11% [8% to 16%]) or meta-analyses (12/183, 7% [4% to 10%]). Overall, the findings suggest that transparent and reproducibility-related research practices are far from routine in psychological science. Future studies can use the present findings as a baseline to assess progress towards increasing the credibility and utility of psychology research.

This video segment, adapted from NOVA, chronicles the education of leading chemist Percy Julian. Although Julian began his elementary school years in the Deep South under Jim Crow laws, he became one of the few African Americans of his time to earn a Ph.D.

Meeting the energy needs of human beings depends on a thorough understanding of the science of energy. Acting to meeting those needs in an environmentally and socially responsible way depends on ethical analysis and spiritual reflection. As with every topic in Healing Earth, today's energy challenges must be approached from the standpoint of an integral ecology--a standpoint that integrates science, ethics, spirituality, and action.

All life depends on Earth's natural resources. In a tragic paradox, human beings are extracting needed, non-renewable resources at a rate that will exhaust the supply for future generations. It is imprudent to place all hope in a technological solution to this paradox. A change in human behavior will have to accompany any realistic attempt to preserve and protect Earth's precious natural resources.

Meeting this challenge must begin with a thorough understanding of the science behind natural resources. Similarly, any proposed actions will require careful ethical analysis and spiritual reflection. As with every topic in Healing Earth, natural resources must be approached from the standpoint of an integral ecology--a standpoint that integrates science, ethics, spirituality, and action.

This chapter of the Healing Earth e-textbook outlines the water's physical structure and characteristics, describes the hydrologic cycle and shows the sources and uses of water. The chapter utilizes the Ignatian pedagogy to further a reader's understanding of water in terms of ethics, spirituality, and action. It includes a case study of the River Ganges.

This 4-lecture series covers the basics of the immune system, how T cells work, how MHC proteins affect our susceptibility to autoimmune diseases, and the relationship between the immune system and infectious diseases.

Library Carpentry lesson to learn how to use the Shell. This Library Carpentry lesson introduces librarians to the Unix Shell. At the conclusion of the lesson you will: understand the basics of the Unix shell; understand why and how to use the command line; use shell commands to work with directories and files; use shell commands to find and manipulate data.

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions. Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks. We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]). Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]). Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed. Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

Software Carpentry lesson on how to use the shell to navigate the filesystem and write simple loops and scripts. The Unix shell has been around longer than most of its users have been alive. It has survived so long because it’s a power tool that allows people to do complex things with just a few keystrokes. More importantly, it helps them combine existing programs in new ways and automate repetitive tasks so they aren’t typing the same things over and over again. Use of the shell is fundamental to using a wide range of other powerful tools and computing resources (including “high-performance computing” supercomputers). These lessons will start you on a path towards using these resources effectively.

Toolkits and eReader Tutorial
Of special importance is this video tutorial for students on how to study from OER materials: Reading on Electronic Devices: A Tutorial (Bonilla 2016).
There are three toolkits: toolkit 1offers relevant materials and resources on:
What is OER? What is an open textbook?
A Bibliography of case studies, user stories, and peer-reviewed articles on adopting OER textbooks and materials
A list of resources for finding OER textbooks and materials
Recommendations on how to advocate for OER adoption to particular audiences (faculty, deans, presidents, and other stakeholders)
Toolkit 2:offers relevant materials and resources on:
Crafting faculty development workshops
Demonstrating faculty use of OER textbooks
Tutorials on finding OER materials once faculty have been identified
Tutorials on student use of OER textbooks
Information on ADA compliance
How to peer review OER materials
Identifying best practices to facilitate OER textbook adoption, implementation, and use
Creating a sustainable OER adoption plan
Toolkit 3: offers relevant materials and resources on:
Offers videos of user stories by faculty who have adopted, implemented, and used OER textbooks
This toolkit also contains ADA compliance reviews of all textbooks that have been reviewed on COOL4Ed

We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository.

Improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. Here we argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. There is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. We discuss the goals of these measures, and how they can be implemented, in the hope that this will facilitate action toward improving the transparency, reproducibility and efficiency of scientific research.