A community-led initiative for training in reproducible research

Auer, Susann; Haelterman, Nele A; Weissberger, Tracey L; Erlich, Jeffrey C; Susilaradeya, Damar; Julkowska, Magdalena; Gazda, Małgorzata Anna; Schwessinger, Benjamin; Jadavji, Nafisa M.; Team, Reproducibility for Everyone; Abitua, Angela; Niraulu, Anzela; Shah, Anshul; Clyburne-Sherinb, April; Guiquel, Benoit; Alicea, Bradly; LaManna, Caroline M.; Ganguly, Diep R; Perkins, Eric; Jambor, Helena; Li, Ian Man Ho; Tsang, Jennifer; Kamens, Joanne; Teytelman, Lenny; Paul, Mariella; Cronin, Michelle; Schmelling, Nicolas; Crisp, Peter A.; Kutum, Rintu; Phuyal, Santosh; Sarabipour, Sarvenaz; Roy, Sonali; Bächle, Susanna M.; Tran, Tuan; Ford, Tyler; Steeves, Vicky; Ilangovan, Vinodh; Baburamani, Ana A.

doi:10.7554/elife.64719

Cited by 16 publications

(7 citation statements)

References 37 publications

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“…Community practice training is also the basis for all public health research, intervention strategy formulation, public health policy implementation, and disaster prevention [ 51 , 52 ]. Applied investigation is also an effective way of health education and health promotion and covers the main contents of practical education and training of community public health [ 53 , 54 ]. The period of major public health events and disease epidemics is the best time for community diagnosis and implementation of public health projects.…”

Section: Discussionmentioning

confidence: 99%

The effect of training medical students in the community area in the midst of the Covid-19 pandemic in China: a community-based study

et al. 2023

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Background Community practice training is an important part of education in medicine, public health, social medicine, and other disciplines. The objective of this study is to explore the effect and importance of the community practice of Master of Public Health graduates on community residents’ health during the Coronavirus Disease 2019 pandemic. Methods This study used a pretest-posttest design. A total of 152 participants with age ≥ 60 years were selected using a multistage sampling method from Hangzhou in China. Baseline and endline data were collected using structured questionnaires by face-to-face interviews. All psychological and behavioral measurements were performed using standardized instruments and showed good reliability and validity. A total of 147 participants were included in the analysis. The chi-square and rank sum tests were used to compare the difference between baseline and endline for categorical variables. Binary logistic regression analysis was used to evaluate the association between community practice training and changes in psychology and behavior. Results The result of chi-square test revealed a statistically significant difference in participants’ eating habits from baseline to endline. Participants reported that the self-perceived health status was different between endline and baseline by the rank sum test. The results of logistic regression analysis showed that community practice training was significantly associated with increased self-efficacy scores, cognitive function and eating habits, with odd ratios of 1.08, 0.90 and 1.93, respectively. Conclusions Community practice training was associated with changes in health behavior and psychology of community residents. Our results suggested enhanced community practice training for students under the Master of Public Health program.

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Section: Discussionmentioning

confidence: 99%

The effect of training medical students in the community area in the midst of the Covid-19 pandemic in China: a community-based study

et al. 2023

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“…There is an increasing need for open and reproducible research practices from scientific societies [14]. Workflow managers have become essential for bioinformatic studies to increase the reproducibility and impact of scientific research [1].…”

Section: Discussionmentioning

confidence: 99%

saks-nf: A json solution for Nextflow pipeline construction

Zhuo

Renzette

Omerza

2022

Preprint

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To address the increasing complexity of data in scientific research, researchers have developed many workflow manager tools. Nextflow is one of the most widely used tools, enabling scalability and reproducibility of scientific workflows across various computational platforms through the implementation of domain-specific language (DSL) with a dataflow paradigm. We developed saks-nf, a JavaScript Object Notation (JSON) solution for constructing Nextflow pipelines. Our solution flattens the learning curve for Nextflow. Users can build and maintain a pipeline without prior programming experience by editing a JSON specification on any text editor. The saks-nf solution can be used to construct a multi-step pipeline with parallel and scatter-gather capacity in a computing platform of choice, such as a local machine, a high-performance cluster, or cloud computing. This solution allows users to focus on analysis, thereby increasing productivity.

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“…For example, The Carpentries Toolkit of IDEAS provides strategies before, during, and after SFT to promote inclusion, diversity, equity, and accessibility (12). In addition to purely technical skills, SFT is also used to disseminate and reinforce professional practices such as research rigor, reproducibility, and other open science skills (13, 14).…”

Section: Introductionmentioning

confidence: 99%

Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond

Williams

Tractenberg

Batut

et al. 2023

Preprint

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Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit its effectiveness and inclusiveness. Prior work including the NSF 2026 Reinventing Scientific Talent proposal called for addressing SFT's challenges, and a diverse international group of experts in education, accessibility, and life sciences came together to do so. This paper describes the phenomenography and content analyses that produced a set of 14 actionable recommendations to systematically strengthen SFT. Recommendations were derived from findings in the educational sciences and the experiences of several of the largest life science SFT programs. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize the training of SFT instructors; deploy SFT to counter inequity). Recommendations are aligned into a purpose-built framework — "The Bicycle Principles" — which prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.

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A community-led initiative for training in reproducible research

Cited by 16 publications

References 37 publications

The effect of training medical students in the community area in the midst of the Covid-19 pandemic in China: a community-based study

The effect of training medical students in the community area in the midst of the Covid-19 pandemic in China: a community-based study

saks-nf: A json solution for Nextflow pipeline construction

Optimizing Short-format Training: an International Consensus on Effective, Inclusive, and Career-spanning Professional Development in the Life Sciences and Beyond

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