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Carpentries Instructor Training

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

Subject:: Computer Science; Information Science; Education; Higher Education; Measurement and Data
Material Type:: Module
Provider:: The Carpentries
Author:: Aleksandra Nenadic; Alexander Konovalov; Alistair John Walsh; Allison Weber; amoskane; Amy E. Hodge; Andrew B. Collier; Anita Schürch; AnnaWilliford; Ariel Rokem; Brian Ballsun-Stanton; Callin Switzer; Christian Brueffer; Christina Koch; Christopher Erdmann; Colin Morris; Dan Allan; DanielBrett; Danielle Quinn; Darya Vanichkina; davidbenncsiro; David Jennings; Eric Jankowski; Erin Alison Becker; Evan Peter Williamson; François Michonneau; Gerard Capes; Greg Wilson; Ian Lee; Jason M Gates; Jason Williams; Jeffrey Oliver; Joe Atzberger; John Bradley; John Pellman; Jonah Duckles; Jonathan Bradley; Karen Cranston; Karen Word; Kari L Jordan; Katherine Koziar; Katrin Leinweber; Kees den Heijer; Laurence; Lex Nederbragt; Maneesha Sane; Marie-Helene Burle; Mik Black; Mike Henry; Murray Cadzow; naught101; Neal Davis; Neil Kindlon; Nicholas Tierney; Nicolás Palopoli; Noah Spies; Paula Andrea Martinez; Petraea; Rayna Michelle Harris; Rémi Emonet; Rémi Rampin; Sarah Brown; Sarah M Brown; Sarah Stevens; satya-vinay; Sean; Serah Anne Njambi Kiburu; Stefan Helfrich; Stéphane Guillou; Steve Moss; Ted Laderas; Tiago M. D. Pereira; Toby Hodges; Tracy Teal; Yo Yehudi
Date Added:: 08/07/2020

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Estimating the prevalence of transparency and reproducibility-related research practices in psychology (2014-2017)

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Estimating the prevalence of transparency and reproducibility-related research practices in psychology (2014-2017)

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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.

Subject:: Psychology
Material Type:: Reading
Author:: Jessica Elizabeth Kosie; john Ioannidis; Joshua D Wallach; Mallory Kidwell; Robert T. Thibault; Tom Elis Hardwicke
Date Added:: 08/07/2020

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Getting an Education

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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.

Subject:: Arts and Humanities; U.S. History
Material Type:: Lecture
Provider:: PBS LearningMedia
Provider Set:: PBS Learning Media Common Core Collection; Teachers' Domain
Author:: The Camille and Henry Dreyfus Foundation; The John D. and Catherine T. MacArthur Foundation; WGBH Educational Foundation
Date Added:: 02/12/2007

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Healing Earth: Energy

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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.

Subject:: Ecology
Material Type:: Textbook
Provider:: Loyola University Chicago
Provider Set:: International Jesuit Ecology Project
Author:: Bill Anderson; Carolyn Martsberger; Christopher Peterson; Clyde Goulden; David Slavsky; George McGraw; Hilly Ann Roa-Quiaoit; Jaime Tatay; Jame Schaefer; Jennifer L. Snyder; Jesse Manuta; Jo Beth D'Agostino; Julie Belandres-Otadoy; Lazar Savari; Leonard Chiti; Luiz Felife Guanaes Rego; Meghan Toomey; Michael Schuck; Nancy Tuchman; Nélida Naveros Córdova; Nicholas Tete; Patrick Daubenmire; Paulus Wiryono; Pedro Linares; Pedro Walpole; Philip Nahlik; Ping Jing; Rachel Hart Winter; Rev. John S.J. Braverman; Shannon Jung; Stephen Mitten; Thomas Lovejoy; Veronica Gaylie; William French
Date Added:: 01/26/2016

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Healing Earth: Natural Resources

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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.

Subject:: Ecology
Material Type:: Textbook
Provider:: Loyola University Chicago
Provider Set:: International Jesuit Ecology Project
Author:: Bill Anderson; Carolyn Martsberger; Christopher Peterson; Clyde Goulden; David Slavsky; George McGraw; Hilly Ann Roa-Quiaoit; Jaime Tatay; Jame Schaefer; Jennifer L. Snyder; Jesse Manuta; Jo Beth D'Agostino; Julie Belandres-Otadoy; Lazar Savari; Leonard Chiti; Luiz Felife Guanaes Rego; Meghan Toomey; Michael Schuck; Nancy Tuchman; Nélida Naveros Córdova; Nicholas Tete; Patrick Daubenmire; Paulus Wiryono; Pedro Linares; Pedro Walpole; Philip Nahlik; Ping Jing; Rachel Hart Winter; Rev. John S.J. Braverman; Shannon Jung; Stephen Mitten; Thomas Lovejoy; Veronica Gaylie; William French
Date Added:: 01/26/2016

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Healing Earth: Water

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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.

Subject:: Ecology
Material Type:: Textbook
Provider:: Loyola University Chicago
Provider Set:: International Jesuit Ecology Project
Author:: Bill Anderson; Carolyn Martsberger; Christopher Peterson; Clyde Goulden; David Slavsky; George McGraw; Hilly Ann Roa-Quiaoit; Jaime Tatay; Jame Schaefer; Jennifer L. Snyder; Jesse Manuta; Jo Beth D'Agostino; Julie Belandres-Otadoy; Lazar Savari; Leonard Chiti; Luiz Felife Guanaes Rego; Meghan Toomey; Michael Schuck; Nancy Tuchman; Nélida Naveros Córdova; Nicholas Tete; Patrick Daubenmire; Paulus Wiryono; Pedro Linares; Pedro Walpole; Philip Nahlik; Ping Jing; Rachel Hart Winter; Rev. John S.J. Braverman; Shannon Jung; Stephen Mitten; Thomas Lovejoy; Veronica Gaylie; William French
Date Added:: 10/07/2015

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Immunology Lecture Series

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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.

Subject:: Health, Medicine and Nursing
Material Type:: Lecture
Provider:: Howard Hughes Medical Institute
Author:: John W. Kappler, Ph.D.; Philippa Marrack, Ph.D.
Date Added:: 04/24/2012

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Library Carpentry: The UNIX Shell

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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.

Subject:: Applied Science; Information Science; Measurement and Data
Material Type:: Module
Provider:: The Carpentries
Author:: Adam Huffman; Alexander Konovalov; Alexander Morley; Alex Kassil; Alex Mendes; Ana Costa Conrado; Andrew Reid; Andrew T. T. McRae; Ariel Rokem; Ashwin Srinath; Bagus Tris Atmaja; Belinda Weaver; Benjamin Bolker; Benjamin Gabriel; BertrandCaron; Brian Ballsun-Stanton; Christopher Erdmann; Christopher Mentzel; colinmorris; Colin Sauze; csqrs; Dan Michael Heggø; Dave Bridges; David McKain; Dmytro Lituiev; earkpr; ekaterinailin; Elena Denisenko; Eric Jankowski; Erin Alison Becker; Evan Williamson; Farah Shamma; Gabriel Devenyi; Gerard Capes; Giuseppe Profiti; Halle Burns; Hannah Burkhardt; hugolio; Ian Lessing; Ian van der Linde; Jake Cowper Szamosi; James Baker; James Guelfi; Jarno Rantaharju; Jarosław Bryk; Jason Macklin; Jeffrey Oliver; jenniferleeucalgary; John Pellman; Jonah Duckles; Jonny Williams; Katrin Leinweber; Kevin M. Buckley; Kunal Marwaha; Laurence; Marc Gouw; Marie-Helene Burle; Marisa Lim; Martha Robinson; Martin Feller; Megan Fritz; Michael Lascarides; Michael Zingale; Michele Hayslett; Mike Henry; Morgan Oneka; Murray Hoggett; Nicolas Barral; Nicola Soranzo; Noah D Brenowitz; Owen Kaluza; Patrick McCann; Peter Hoyt; Rafi Ullah; Raniere Silva; Rémi Emonet; reshama shaikh; Ruud Steltenpool; sjnair; Stéphane Guillou; Stephan Schmeing; Stephen Jones; Stephen Leak; Susan J Miller; Thomas Mellan; Tim Dennis; Tom Dowrick; Travis Lilleberg; Victor Koppejan; Vikram Chhatre; Yee Mey
Date Added:: 08/07/2020

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Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

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Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

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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.

Subject:: Biology
Material Type:: Reading
Provider:: PLOS Biology
Author:: John P. A. Ioannidis; Joshua D. Wallach; Kevin W. Boyack
Date Added:: 08/07/2020

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Scientific Processes

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In this interactive activity adapted from NOVA, expand your understanding of the scientific process. Watch two videos featuring animations and interviews with scientists, and notice how the processes unfold and vary from one investigation to the other.

Subject:: Life Science; Chemistry; Physics
Material Type:: Activity/Lab; Interactive
Provider:: PBS LearningMedia
Provider Set:: PBS Learning Media Common Core Collection; Teachers' Domain
Author:: The Camille and Henry Dreyfus Foundation; The John D. and Catherine T. MacArthur Foundation; WGBH Educational Foundation
Date Added:: 08/01/2007

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The Unix Shell

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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.

Subject:: Computer Science; Measurement and Data
Material Type:: Module
Provider:: The Carpentries
Author:: Adam Huffman; Adam James Orr; Adam Richie-Halford; AidaMirsalehi; Alexander Konovalov; Alexander Morley; Alex Kassil; Alex Mac; Alix Keener; Amy Brown; Andrea Bedini; Andrew Boughton; Andrew Reid; Andrew T. T. McRae; Andrew Walker; Ariel Rokem; Armin Sobhani; Ashwin Srinath; Bagus Tris Atmaja; Bartosz Telenczuk; Ben Bolker; Benjamin Gabriel; Bertie Seyffert; Bill Mills; Brian Ballsun-Stanton; BrianBill; Camille Marini; Chris Mentzel; Christina Koch; Colin Morris; Colin Sauze; csqrs; Damien Irving; Dana Brunson; Daniel Baird; Danielle M. Nielsen; Daniel McCloy; Daniel Standage; Dan Jones; Dave Bridges; David Eyers; David McKain; David Vollmer; Dean Attali; Devinsuit; Dmytro Lituiev; Donny Winston; Doug Latornell; Dustin Lang; earkpr; ekaterinailin; Elena Denisenko; Emily Dolson; Emily Jane McTavish; Eric Jankowski; Erin Alison Becker; Ethan P White; Evgenij Belikov; Farah Shamma; Fatma Deniz; Filipe Fernandes; Francis Gacenga; François Michonneau; Gabriel A. Devenyi; Gerard Capes; Giuseppe Profiti; Greg Wilson; Halle Burns; Hannah Burkhardt; Harriet Alexander; Hugues Fontenelle; Ian van der Linde; Inigo Aldazabal Mensa; Jackie Milhans; Jake Cowper Szamosi; James Guelfi; Jan T. Kim; Jarek Bryk; Jarno Rantaharju; Jason Macklin; Jay van Schyndel; Jens vdL; John Blischak; John Pellman; John Simpson; Jonah Duckles; Jonny Williams; Joshua Madin; Kai Blin; Kathy Chung; Katrin Leinweber; Kevin M. Buckley; Kirill Palamartchouk; Klemens Noga; Kristopher Keipert; Kunal Marwaha; Laurence; Lee Zamparo; Lex Nederbragt; Mahdi Sadjadi; Marcel Stimberg; Marc Rajeev Gouw; Maria Doyle; Marie-Helene Burle; Marisa Lim; Mark Mandel; Martha Robinson; Martin Feller; Matthew Gidden; Matthew Peterson; M Carlise; Megan Fritz; Michael Zingale; Mike Henry; Mike Jackson; Morgan Oneka; Murray Hoggett; Nicolas Barral; Nicola Soranzo; Noah D Brenowitz; Noam Ross; Norman Gray; nther; Orion Buske; Owen Kaluza; Patrick McCann; Paul Gardner; Pauline Barmby; Peter R. Hoyt; Peter Steinbach; Philip Lijnzaad; Phillip Doehle; Piotr Banaszkiewicz; Rafi Ullah; Raniere Silva; Rémi Emonet; reshama shaikh; Robert A Beagrie; Ruud Steltenpool; Ry4an Brase; Sarah Mount; Sarah Simpkin; s-boardman; Scott Ritchie; sjnair; Stéphane Guillou; Stephan Schmeing; Stephen Jones; Stephen Turner; Steve Leak; Susan Miller; Thomas Mellan; Tim Keighley; Tobin Magle; Tom Dowrick; Trevor Bekolay; Varda F. Hagh; Victor Koppejan; Vikram Chhatre; Yee Mey
Date Added:: 03/20/2017

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WHCL Open Educational Resources

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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

Subject:: Education
Material Type:: Primary Source; Reading
Author:: British Columbia Open Textbook Project; I Elaine Allen Jeff Seaman; John D; This page is an adaption of Lansing Community College (LCC) Library Research Guide on Open Educational Resources (OER) by Regina Gong is licensed under a Creative Commons Attribution 4.0 International License.
Date Added:: 02/21/2019

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A consensus-based transparency checklist

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A consensus-based transparency checklist

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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.

Subject:: Psychology
Material Type:: Reading
Provider:: Nature Human Behaviour
Author:: Agneta Fisher; Alexandra M. Freund; Alexandra Sarafoglou; Alice S. Carter; Andrew A. Bennett; Andrew Gelman; Balazs Aczel; Barnabas Szaszi; Benjamin R. Newell; Brendan Nyhan; Candice C. Morey; Charles Clifton; Christopher Beevers; Christopher D. Chambers; Christopher Sullivan; Cristina Cacciari; Daniel Benjamin; Daniel J. Simons; David R. Shanks; Debra Lieberman; Derek Isaacowitz; Dolores Albarracin; Don P. Green; D. Stephen Lindsay; Eric-Jan Wagenmakers; Eric Johnson; Eveline A. Crone; Fernando Hoces de la Guardia; Fiammetta Cosci; George C. Banks; Gordon D. Logan; Hal R. Arkes; Harold Pashler; Janet Kolodner; Jarret Crawford; Jeffrey Pollack; Jelte M. Wicherts; John Antonakis; John Curtin; John P. Ioannidis; Joseph Cesario; Kai Jonas; Lea Moersdorf; Lisa L. Harlow; Marcus Munafò; Mark Fichman; M. Gareth Gaskell; Mike Cortese; Mitja D. Back; Morton A. Gernsbacher; Nelson Cowan; Nicole D. Anderson; Pasco Fearon; Randall Engle; Robert L. Greene; Roger Giner-Sorolla; Ronán M. Conroy; Scott O. Lilienfeld; Simine Vazire; Simon Farrell; Šimon Kucharský; Stavroula Kousta; Ty W. Boyer; Wendy B. Mendes; Wiebke Bleidorn; Willem Frankenhuis; Zoltan Kekecs
Date Added:: 08/07/2020

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A manifesto for reproducible science

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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.

Subject:: Social Science
Material Type:: Reading
Provider:: Nature Human Behaviour
Author:: Brian A. Nosek; Christopher D. Chambers; Dorothy V. M. Bishop; Eric-Jan Wagenmakers; Jennifer J. Ware; John P. A. Ioannidis; Katherine S. Button; Marcus R. Munafò; Nathalie Percie du Sert; Uri Simonsohn
Date Added:: 08/07/2020

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