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Carpentries Instructor Training
Unrestricted Use
CC BY
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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
Estimating the prevalence of transparency and reproducibility-related research practices in psychology (2014-2017)
Unrestricted Use
CC BY
Rating

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
Getting an Education
Read the Fine Print
Educational Use
Rating

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
Healing Earth: Energy
Only Sharing Permitted
CC BY-NC-ND
Rating

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
Healing Earth: Natural Resources
Only Sharing Permitted
CC BY-NC-ND
Rating

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
Healing Earth: Water
Only Sharing Permitted
CC BY-NC-ND
Rating

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
Immunology Lecture Series
Restricted Use
Copyright Restricted
Rating

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
Library Carpentry: The UNIX Shell
Unrestricted Use
CC BY
Rating

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
Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017
Unrestricted Use
CC BY
Rating

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
Scientific Processes
Read the Fine Print
Educational Use
Rating

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
The Unix Shell
Unrestricted Use
CC BY
Rating

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
WHCL Open Educational Resources
Unrestricted Use
CC BY
Rating

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
A consensus-based transparency checklist
Unrestricted Use
CC BY
Rating

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
A manifesto for reproducible science
Unrestricted Use
CC BY
Rating

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