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.

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.

(This case study was added to OER Commons as one of a batch of over 700. It has relevant information which may include medical imagery, lab results, and history where relevant. A link to the final diagnosis can be found at the end of the case study for review. The first paragraph of the case study -- typically, but not always the clinical presentation -- is provided below.)

A 46-year-old man presented with a 2 week history of bilateral lower extremity numbness and tingling. The patient had a past medical history significant for a right posterior fossa medulloblastoma diagnosed at the age of 24, treated with total resection and craniospinal radiation (5040 cGy to the posterior fossa, 3960 cGy to the whole brain, and 3420 cGy to the spine). Twenty-one years later, at the age of 45, the patient experienced progressive right lower extremity weakness and subsequent MRI showed an expansile intradural extramedullary enhancing 1.3 cm T5 level spinal cord lesion. This lesion was presumed to be recurrent medulloblastoma in the form of drop metastasis, and the patient underwent additional radiation to the tumor and a small surrounding margin (3750 cGy). Several months after treatment, at the age of 46, the patient experienced recurrent symptoms of lower leg weakness. A follow-up MRI revealed a 1.4 cm intradural extramedullary lesion at T7 with associated cord edema. Sagittal sequences performed after the administration of intravenous gadolinium chelate demonstrated subtle enhancement (Figure 1). In an effort to confirm the diagnosis of recurrent meduloblastoma and rule out radiation necrosis or a second malignancy as well as to help determine future treatment it was determined that histological confirmation was necessary. The patient underwent an uneventful thoracic laminectomy at T6-T7 with subtotal resection of the intradural lesion.

(This case study was added to OER Commons as one of a batch of over 700. It has relevant information which may include medical imagery, lab results, and history where relevant. A link to the final diagnosis can be found at the end of the case study for review. The first paragraph of the case study -- typically, but not always the clinical presentation -- is provided below.)

A female in her 50's with a known history of neurofibromatosis type 1 since childhood, and a number of previously resected neurofibromas, presented with an enlarging right flank mass concerning for a plexiform neurofibroma. A computed tomography (CT) abdomen and pelvis with contrast demonstrated a cystic mass measuring up to 7.4 cm within the right abdominal wall (Figure 1, A) with areas of calcification and enhancement.

(This case study was added to OER Commons as one of a batch of over 700. It has relevant information which may include medical imagery, lab results, and history where relevant. A link to the final diagnosis can be found at the end of the case study for review. The first paragraph of the case study -- typically, but not always the clinical presentation -- is provided below.)

This elderly man had a medical and oncologic history significant for a myeloproliferative disorder in the remote past, chronic lymphocytic leukemia, recurrent osteochondroma, prostatic adenocarcinoma, renal insufficiency and coronary artery disease. Past surgical history is notable for a left nephrectomy for "benign" renal disease 28 years earlier and partial colectomy for severe polyposis. He presented for total hip replacement due to worsening hip pain unresponsive to analgesic treatments leaving him virtually bedridden. Several days before his admission, he developed nausea and vomiting with loss of appetite and indeterminate weight loss. Physical examination showed only a slightly enlarged prostate and an abdominal hernia. No abdominal masses or lymphadenopathy were appreciated. Laboratory evaluation then included a complete blood count showing a white blood cell count of 50,700/cu mm with a differential of 6% polymorphonuclear leucocytes, 89% lymphocytes, 3% monocytes, 1% eosinophils, and 1% basophils. Hemoglobin was 11.6 g/dl and platelet count 168,000/cu mm. Electrolytes were within normal limits. Blood urea nitrogen was 32 mg/dl and creatinine 1.7 mg/dl. Liver enzymes, alkaline phosphatase, and total bilirubin were within normal limits. Albumin was marginally low at 3.1 g/dl. Prostatic specific antigen level was 0.1 ng/ml. An abdominal and retroperitoneal ultrasound was performed revealing a 12 cm by 9.5 cm lobulated, hypoechoic soft tissue mass with central necrosis in the right suprarenal region. Subsequent computed tomography scan demonstrated a 10.3 cm by 9.3 cm lobulated heterogeneous right adrenal mass. The mass displaced the right kidney posteriorly and inferiorly with focal compression of the inferior vena cava and extending to the renal hilum (Figures 1A, 1B, and 1C). CT guided biopsy of the mass was diagnosed as cytologically and histologically bland adrenal cortical tissue. The patient subsequently underwent exploratory laparotomy with resection of the adrenal mass. Intraoperatively, a large necrotic appearing tumor encompassed the right adrenal gland, but extended to and was fixed to the inferior vena cava. The tumor was also seen to extend under the right renal vein and involve the right renal hilum. The tumor was incompletely resected secondary to fixation to adjacent structures and intraoperative hemorrhage. This final pathologic diagnosis in this case was based on a compilation of pathologic data including immunohistochemistry, electron microscopy, and mutational profiling.

(This case study was added to OER Commons as one of a batch of over 700. It has relevant information which may include medical imagery, lab results, and history where relevant. A link to the final diagnosis can be found at the end of the case study for review. The first paragraph of the case study -- typically, but not always the clinical presentation -- is provided below.)

The patient was an elderly man in his 80s who presented with dyspnea, fatigue, and subacute weight loss. Imaging identified a large left lower lobe mass with mediastinal lymphadenopathy. A CT-guided biopsy was performed, which identified a poorly differentiated adenocarcinoma (Figure 1) which was positive for CK7 and TTF-1 but negative for CK5/6 and p40, consistent with lung origin. Ancillary testing was performed, and the tumor cells were positive for PD-L1 (TPS 50%) and negative for ALK by immunohistochemistry (IHC). Fluorescence in-situ hybridization (FISH) was negative for ALK rearrangement (other targets failed). Oncomine next generation sequencing (NGS) was also performed, which identified a TP53 mutation, MET splice site mutation near codon D981, and "fusion" adjoining exons 13 and 15 of MET (Figures 2 and 3).

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.

This unit is designed to function as three days of instruction in an introductory urban planning, environmental science/studies or public health course.

(Note: this resource was added to OER Commons as part of a batch upload of over 2,200 records. If you notice an issue with the quality of the metadata, please let us know by using the 'report' button and we will flag it for consideration.)

The introduction and examination of the food, energy, and water connection -- as a system in Unit 1 -- established the dictates of human dependency on and human modification of the environment. We continue a logical progression of what this means in Unit 2, with a focus on how people see, confront, and solve their resource challenges in the light of their need for affordable, accessible, healthy, sustainably-grown food. This unit introduces and explores the concepts, themes, and practices of: urban agriculture, urban farming, local food, food insecurity, food deserts, health & wellness education, community food gardens, community food dialogue, public policy, civic engagement, volunteerism, expert technical assistance, land reclamation, grants and incentives, entrepreneurship, and community economic development.

(Note: this resource was added to OER Commons as part of a batch upload of over 2,200 records. If you notice an issue with the quality of the metadata, please let us know by using the 'report' button and we will flag it for consideration.)

In the capstone, Unit 3, students are provided a real-world example of local community action to address the challenge of "healthy food access." The 2015 Leon County (Florida) Sustainable Communities Summit highlights the results of communities working together to promote environmental and food justice. By the end of Unit 3, instructors can deliver a call to action to empower students to be participatory citizens in their communities. The summative assessment will evaluate the students' ability to synthesize the module learning objectives and demonstrate the use of science practices.

(Note: this resource was added to OER Commons as part of a batch upload of over 2,200 records. If you notice an issue with the quality of the metadata, please let us know by using the 'report' button and we will flag it for consideration.)

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

Deficiencies in methods reporting in animal experimentation lead to difficulties in reproducing experiments; the authors propose a set of reporting standards to improve scientific communication and study design. The US National Institute of Neurological Disorders and Stroke convened major stakeholders in June 2012 to discuss how to improve the methodological reporting of animal studies in grant applications and publications. The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data. We recognize that achieving a meaningful improvement in the quality of reporting will require a concerted effort by investigators, reviewers, funding agencies and journal editors. Requiring better reporting of animal studies will raise awareness of the importance of rigorous study design to accelerate scientific progress.

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.