1
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Reyes RJ, Pham O, Fergusson R, Ceberio N, Clark C, Sarah Cohen C, Fuse M, Pennings P. SCIP: a self-paced, community-based summer coding program creates community and increases coding confidence, lessons learned from the pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.12.27.521952. [PMID: 36597523 PMCID: PMC9810221 DOI: 10.1101/2022.12.27.521952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In 2020, many students lost summer opportunities due to the COVID-19 pandemic. We wanted to offer students an opportunity to learn computational skills and be part of a community while they were stuck at home. Because the pandemic was very isolating, it was important to support students to learn and build community online. We used lessons learned from literature and our own experience to design, run and test an online program for students called the Science Coding Immersion Program (SCIP). In our program, students worked in small teams for 8 hours a week spread over the week, with one participant as the team leader and Zoom host. Teams worked on an online R or Python class at their own pace with support on Slack from the organizing team. For motivation and career advice, we hosted a weekly webinar with guest speakers. We used pre- and post-program surveys to determine how different aspects of the program impacted students. We were able to recruit a large and diverse group of participants who were happy with the program, found community in their team, and improved their coding confidence. We hope that our work will inspire others to start their own version of SCIP.
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Affiliation(s)
| | - Olivia Pham
- Biology Department, San Francisco State University, San Francisco, CA
| | - Ryan Fergusson
- Biology Department, San Francisco State University, San Francisco, CA
| | - Niquo Ceberio
- Biology Department, San Francisco State University, San Francisco, CA
| | - Candace Clark
- Biology Department, San Francisco State University, San Francisco, CA
| | - C Sarah Cohen
- Biology Department, San Francisco State University, San Francisco, CA
| | - Megumi Fuse
- Biology Department, San Francisco State University, San Francisco, CA
| | - Pleuni Pennings
- Biology Department, San Francisco State University, San Francisco, CA
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2
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Williams JJ, Tractenberg RE, Batut B, Becker EA, Brown AM, Burke ML, Busby B, Cooch NK, Dillman AA, Donovan SS, Doyle MA, van Gelder CWG, Hall CR, Hertweck KL, Jordan KL, Jungck JR, Latour AR, Lindvall JM, Lloret-Llinares M, McDowell GS, Morris R, Mourad T, Nisselle A, Ordóñez P, Paladin L, Palagi PM, Sukhai MA, Teal TK, Woodley L. An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. PLoS One 2023; 18:e0293879. [PMID: 37943810 PMCID: PMC10635508 DOI: 10.1371/journal.pone.0293879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
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 SFT's effectiveness and inclusiveness. Education researchers, students in SFT courses, and organizations have called for research and strategies that can strengthen SFT in terms of effectiveness, inclusiveness, and accessibility across multiple dimensions. This paper describes the project that resulted in a consensus set of 14 actionable recommendations to systematically strengthen SFT. A diverse international group of 30 experts in education, accessibility, and life sciences came together from 10 countries to develop recommendations that can help strengthen SFT globally. Participants, including representation from some of the largest life science training programs globally, assembled findings in the educational sciences and encompassed the experiences of several of the largest life science SFT programs. The 14 recommendations were derived through a Delphi method, where consensus was achieved in real time as the group completed a series of meetings and tasks designed to elicit specific recommendations. 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 training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned with a purpose-built framework-"The Bicycle Principles"-that 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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Affiliation(s)
- Jason J. Williams
- DNA Learning Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Rochelle E. Tractenberg
- Collaborative for Research on Outcomes and Metrics, Georgetown University, Washington, DC, United States of America
| | - Bérénice Batut
- Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Open Life Science, Freiburg, Germany
| | | | - Anne M. Brown
- Virginia Tech, Blacksburg, Virginia, United States of America
| | - Melissa L. Burke
- Australian BioCommons, North Melbourne, Australia
- Queensland Cyber Infrastructure Foundation, Research Computing Centre
- The University of Queensland
| | - Ben Busby
- DNAnexus, Mountain View, California, United States of America
| | | | | | | | | | | | - Christina R. Hall
- Australian BioCommons, North Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Kate L. Hertweck
- Chan Zuckerberg Initiative, Redwood City, California, United States of America
| | | | - John R. Jungck
- University of Delaware, Newark, DE, United States of America
| | | | | | - Marta Lloret-Llinares
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Gary S. McDowell
- Lightoller LLC
- The Ronin Institute, Montclair, NJ, United States of America
- Institute for Globally Distributed Open Research and Education
| | - Rana Morris
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
| | - Teresa Mourad
- Ecological Society of America, Washington, DC, United States of America
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Melbourne, Australia
- Melbourne Genomics, The University of Melbourne, Melbourne, Australia
| | - Patricia Ordóñez
- University of Maryland Baltimore County, Catonsville, Maryland, United States of America
| | - Lisanna Paladin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | | | - Mahadeo A. Sukhai
- Canadian National Institute for the Blind, Toronto, Canada
- Queen’s University School of Medicine, Kingston, Canada
| | - Tracy K. Teal
- Posit, PBC, Boston, Massachusetts, United States of America
| | - Louise Woodley
- Center for Scientific Collaboration and Community Engagement, Oakland, California, United States of America
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3
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Kelliher JM, Rudolph M, Vangay P, Abbas A, Borton MA, Davenport ER, Davenport KW, Erazo NG, Herman C, Karstens L, Kocurek B, Lutz HL, Myers KS, Ockert I, Rodriguez FE, Santistevan C, Saunders JK, Smith ML, Vogtmann E, Windsor A, Wood-Charlson EM, Woodley L, Eloe-Fadrosh EA. Cohort-based learning for microbiome research community standards. Nat Microbiol 2023; 8:751-753. [PMID: 37069400 DOI: 10.1038/s41564-023-01361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Affiliation(s)
| | - Marisa Rudolph
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pajau Vangay
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Arwa Abbas
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | - Natalia G Erazo
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
| | | | - Lisa Karstens
- Oregon Health and Science University, Portland, OR, USA
| | - Brandon Kocurek
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, USA
| | | | - Kevin S Myers
- Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ingrid Ockert
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Camille Santistevan
- Center for Scientific Collaboration and Community Engagement, Oakland, CA, USA
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution, Falmouth, MA, USA
- University of Georgia, Athens, GA, USA
| | | | | | - Amanda Windsor
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | | | - Lou Woodley
- Center for Scientific Collaboration and Community Engagement, Oakland, CA, USA
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4
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Gaynor KM, Azevedo T, Boyajian C, Brun J, Budden AE, Cole A, Csik S, DeCesaro J, Do-Linh H, Dudney J, Galaz García C, Leonard S, Lyon NJ, Marks A, Parish J, Phillips AA, Scarborough C, Smith J, Thompson M, Vargas Poulsen C, Fong CR. Ten simple rules to cultivate belonging in collaborative data science research teams. PLoS Comput Biol 2022; 18:e1010567. [PMID: 36327241 PMCID: PMC9632775 DOI: 10.1371/journal.pcbi.1010567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Kaitlyn M. Gaynor
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
- Departments of Zoology and Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Therese Azevedo
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Clarissa Boyajian
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Julien Brun
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Amber E. Budden
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
- Main Library, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Allie Cole
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Samantha Csik
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Joe DeCesaro
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Halina Do-Linh
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Joan Dudney
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Carmen Galaz García
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Scout Leonard
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Nicholas J. Lyon
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Althea Marks
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Julia Parish
- Bren School of Environmental Science and Management, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Alexandra A. Phillips
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Courtney Scarborough
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Joshua Smith
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Marcus Thompson
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Camila Vargas Poulsen
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Caitlin R. Fong
- National Center for Ecological Analysis and Synthesis, University of California Santa Barbara, Santa Barbara, California, United States of America
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5
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Zuckerman AL, Lo SM. Examining the Variations in Undergraduate Students' Conceptions of Successful Researchers: A Phenomenographic Study. CBE LIFE SCIENCES EDUCATION 2022; 21:ar55. [PMID: 35925918 PMCID: PMC9582811 DOI: 10.1187/cbe.21-10-0295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Undergraduate education represents an important transitional stage in which students make career decisions, and undergraduate research experiences (UREs) play a critical role in training the next generation of science, technology, engineering, and mathematics researchers. Extensive studies have identified the different ways in which researchers and graduate students understand their profession, but little work has focused on undergraduate students. To contribute to this gap in literature, this study examines how undergraduate students conceptualize successful researchers. Data were collected using semistructured interviews with transfer students at a research-intensive university, in which participants articulated how they perceive a successful researcher and how their conception had changed based on their undergraduate experiences. Using phenomenography as the research approach, three conceptions of successful researchers were identified based on variations within the following aspects: process of research, interactions with other researchers, and scope of contribution. Retrospective conceptions were more simplistic, with little appreciation for the complex methodological processes and collaborations needed to meaningfully contribute to the research community. After UREs, participants reported conceptions with more nuanced understanding that successful researchers demonstrate proactive engagement, collaboration, and contribution. These findings can be applied to facilitate meaningful research experiences and target undergraduates' professional development as they are enculturated into the research community.
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Affiliation(s)
- Austin L. Zuckerman
- Department of Cell and Developmental Biology, School of Biological Sciences, and Program in Mathematics and Science Education, University of California San Diego, La Jolla, CA 92093
- Program in Mathematics and Science Education, San Diego State University, San Diego, CA 92120
| | - Stanley M. Lo
- Department of Cell and Developmental Biology, School of Biological Sciences, and Program in Mathematics and Science Education, University of California San Diego, La Jolla, CA 92093
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6
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Rosenfeld DL, Balcetis E, Bastian B, Berkman ET, Bosson JK, Brannon TN, Burrow AL, Cameron CD, Chen S, Cook JE, Crandall C, Davidai S, Dhont K, Eastwick PW, Gaither SE, Gangestad SW, Gilovich T, Gray K, Haines EL, Haselton MG, Haslam N, Hodson G, Hogg MA, Hornsey MJ, Huo YJ, Joel S, Kachanoff FJ, Kraft-Todd G, Leary MR, Ledgerwood A, Lee RT, Loughnan S, MacInnis CC, Mann T, Murray DR, Parkinson C, Pérez EO, Pyszczynski T, Ratner K, Rothgerber H, Rounds JD, Schaller M, Silver RC, Spellman BA, Strohminger N, Swim JK, Thoemmes F, Urganci B, Vandello JA, Volz S, Zayas V, Tomiyama AJ. Psychological Science in the Wake of COVID-19: Social, Methodological, and Metascientific Considerations. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2022; 17:311-333. [PMID: 34597198 PMCID: PMC8901450 DOI: 10.1177/1745691621999374] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The COVID-19 pandemic has extensively changed the state of psychological science from what research questions psychologists can ask to which methodologies psychologists can use to investigate them. In this article, we offer a perspective on how to optimize new research in the pandemic's wake. Because this pandemic is inherently a social phenomenon-an event that hinges on human-to-human contact-we focus on socially relevant subfields of psychology. We highlight specific psychological phenomena that have likely shifted as a result of the pandemic and discuss theoretical, methodological, and practical considerations of conducting research on these phenomena. After this discussion, we evaluate metascientific issues that have been amplified by the pandemic. We aim to demonstrate how theoretically grounded views on the COVID-19 pandemic can help make psychological science stronger-not weaker-in its wake.
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Affiliation(s)
| | | | - Brock Bastian
- Melbourne School of Psychological Sciences, University of Melbourne
| | - Elliot T. Berkman
- Department of Psychology, University of Oregon
- Center for Translational Neuroscience, University of Oregon
| | | | | | | | - C. Daryl Cameron
- Department of Psychology, The Pennsylvania State University
- Rock Ethics Institute, The Pennsylvania State University
| | - Serena Chen
- Department of Psychology, University of California, Berkeley
| | | | | | | | | | | | | | | | | | - Kurt Gray
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill
| | | | - Martie G. Haselton
- Department of Psychology, University of California, Los Angeles
- Department of Communication, University of California, Los Angeles
- Institute for Society and Genetics, University of California, Los Angeles
| | - Nick Haslam
- Melbourne School of Psychological Sciences, University of Melbourne
| | | | | | | | - Yuen J. Huo
- Department of Psychology, University of California, Los Angeles
| | | | - Frank J. Kachanoff
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill
| | | | - Mark R. Leary
- Department of Psychology and Neuroscience, Duke University
| | | | | | - Steve Loughnan
- School of Philosophy, Psychology, and Language Sciences, The University of Edinburgh
| | | | - Traci Mann
- Department of Psychology, University of Minnesota
| | | | | | - Efrén O. Pérez
- Department of Psychology, University of California, Los Angeles
- Department of Political Science, University of California, Los Angeles
| | - Tom Pyszczynski
- Department of Psychology, University of Colorado at Colorado Springs
| | | | | | | | - Mark Schaller
- Department of Psychology, University of British Columbia
| | - Roxane Cohen Silver
- Department of Psychological Science, University of California, Irvine
- Department of Medicine, University of California, Irvine
- Program in Public Health, University of California, Irvine
| | | | - Nina Strohminger
- Department of Legal Studies and Business Ethics, Wharton School of Business, University of Pennsylvania
- Department of Psychology, University of Pennsylvania
| | - Janet K. Swim
- Department of Psychology, The Pennsylvania State University
| | - Felix Thoemmes
- Department of Human Development, Cornell University
- Department of Psychology, Cornell University
| | | | | | - Sarah Volz
- Department of Psychology, University of Minnesota
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7
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Holmgren SD, Boyles RR, Cronk RD, Duncan CG, Kwok RK, Lunn RM, Osborn KC, Thessen AE, Schmitt CP. Catalyzing Knowledge-Driven Discovery in Environmental Health Sciences through a Community-Driven Harmonized Language. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:8985. [PMID: 34501574 PMCID: PMC8430534 DOI: 10.3390/ijerph18178985] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 01/10/2023]
Abstract
Harmonized language is critical for helping researchers to find data, collecting scientific data to facilitate comparison, and performing pooled and meta-analyses. Using standard terms to link data to knowledge systems facilitates knowledge-driven analysis, allows for the use of biomedical knowledge bases for scientific interpretation and hypothesis generation, and increasingly supports artificial intelligence (AI) and machine learning. Due to the breadth of environmental health sciences (EHS) research and the continuous evolution in scientific methods, the gaps in standard terminologies, vocabularies, ontologies, and related tools hamper the capabilities to address large-scale, complex EHS research questions that require the integration of disparate data and knowledge sources. The results of prior workshops to advance a harmonized environmental health language demonstrate that future efforts should be sustained and grounded in scientific need. We describe a community initiative whose mission was to advance integrative environmental health sciences research via the development and adoption of a harmonized language. The products, outcomes, and recommendations developed and endorsed by this community are expected to enhance data collection and management efforts for NIEHS and the EHS community, making data more findable and interoperable. This initiative will provide a community of practice space to exchange information and expertise, be a coordination hub for identifying and prioritizing activities, and a collaboration platform for the development and adoption of semantic solutions. We encourage anyone interested in advancing this mission to engage in this community.
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Affiliation(s)
- Stephanie D. Holmgren
- Office of Data Science, National Institute of Environmental Health Sciences (NIEHS), Durham, NC 27709, USA;
| | | | | | - Christopher G. Duncan
- Genes, Environment, and Health Branch, Division of Extramural Research and Training, NIEHS, Durham, NC 27709, USA;
| | - Richard K. Kwok
- Epidemiology Branch, Division of Intramural Research, NIEHS, Durham, NC 27709, USA;
- Office of the Director, NIEHS, Bethesda, MD 20892, USA
| | - Ruth M. Lunn
- Integrative Health Assessment Branch, Division of the National Toxicology Program, NIEHS, Durham, NC 27709, USA;
| | | | - Anne E. Thessen
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR 97331, USA;
| | - Charles P. Schmitt
- Office of Data Science, National Institute of Environmental Health Sciences (NIEHS), Durham, NC 27709, USA;
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8
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Hall CR, Griffin PC, Lonie AJ, Christiansen JH. Application of a bioinformatics training delivery method for reaching dispersed and distant trainees. PLoS Comput Biol 2021; 17:e1008715. [PMID: 33735276 PMCID: PMC7971692 DOI: 10.1371/journal.pcbi.1008715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many initiatives have addressed the global need to upskill biologists in bioinformatics tools and techniques. Australia is not unique in its requirement for such training, but due to its large size and relatively small and geographically dispersed population, Australia faces specific challenges. A combined training approach was implemented by the authors to overcome these challenges. The “hybrid” method combines guidance from experienced trainers with the benefits of both webinar-style delivery and concurrent face-to-face hands-on practical exercises in classrooms. Since 2017, the hybrid method has been used to conduct 9 hands-on bioinformatics training sessions at international scale in which over 800 researchers have been trained in diverse topics on a range of software platforms. The method has become a key tool to ensure scalable and more equitable delivery of short-course bioinformatics training across Australia and can be easily adapted to other locations, topics, or settings.
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Affiliation(s)
- Christina R. Hall
- Australian BioCommons, Australia
- EMBL Australia Bioinformatics Resource, Australia
- Melbourne Bioinformatics, University of Melbourne, Victoria, Australia
- * E-mail:
| | - Philippa C. Griffin
- Australian BioCommons, Australia
- EMBL Australia Bioinformatics Resource, Australia
- Melbourne Bioinformatics, University of Melbourne, Victoria, Australia
| | - Andrew J. Lonie
- Australian BioCommons, Australia
- EMBL Australia Bioinformatics Resource, Australia
- Melbourne Bioinformatics, University of Melbourne, Victoria, Australia
| | - Jeffrey H. Christiansen
- Australian BioCommons, Australia
- EMBL Australia Bioinformatics Resource, Australia
- Research Computing Centre, The University of Queensland, Queensland, Australia
- Queensland Cyber Infrastructure Foundation, Queensland, Australia
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9
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Reiter T, Brooks† PT, Irber† L, Joslin† SEK, Reid† CM, Scott† C, Brown CT, Pierce-Ward NT. Streamlining data-intensive biology with workflow systems. Gigascience 2021; 10:giaa140. [PMID: 33438730 PMCID: PMC8631065 DOI: 10.1093/gigascience/giaa140] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/14/2022] Open
Abstract
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these practices in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.
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Affiliation(s)
- Taylor Reiter
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Phillip T Brooks†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Luiz Irber†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Shannon E K Joslin†
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles M Reid†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Camille Scott†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - N Tessa Pierce-Ward
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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10
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Jiménez-García B, Teixeira JMC, Trellet M, Rodrigues JPGLM, Bonvin AMJJ. PDB-tools web: A user-friendly interface for the manipulation of PDB files. Proteins 2020; 89:330-335. [PMID: 33111403 PMCID: PMC7855443 DOI: 10.1002/prot.26018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/06/2023]
Abstract
The Protein Data Bank (PDB) file format remains a popular format used and supported by many software to represent coordinates of macromolecular structures. It however suffers from drawbacks such as error‐prone manual editing. Because of that, various software toolkits have been developed to facilitate its editing and manipulation, but, to date, there is no online tool available for this purpose. Here we present PDB‐Tools Web, a flexible online service for manipulating PDB files. It offers a rich and user‐friendly graphical user interface that allows users to mix‐and‐match more than 40 individual tools from the pdb‐tools suite. Those can be combined in a few clicks to perform complex pipelines, which can be saved and uploaded. The resulting processed PDB files can be visualized online and downloaded. The web server is freely available at https://wenmr.science.uu.nl/pdbtools.
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Affiliation(s)
- Brian Jiménez-García
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - João M C Teixeira
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mikael Trellet
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - João P G L M Rodrigues
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA
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11
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Beck MW, O’Hara C, Stewart Lowndes JS, D. Mazor R, Theroux S, J. Gillett D, Lane B, Gearheart G. The importance of open science for biological assessment of aquatic environments. PeerJ 2020; 8:e9539. [PMID: 32742805 PMCID: PMC7377246 DOI: 10.7717/peerj.9539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/23/2020] [Indexed: 11/22/2022] Open
Abstract
Open science principles that seek to improve science can effectively bridge the gap between researchers and environmental managers. However, widespread adoption has yet to gain traction for the development and application of bioassessment products. At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing. In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive condition assessments and proactive applications that inform environmental management. An example from the state of California demonstrates effective adoption of open science principles through data stewardship, reproducible research, and engagement of stakeholders with multimedia applications. We also discuss technical, sociocultural, and institutional challenges for adopting open science, including practical approaches for overcoming these hurdles in bioassessment applications.
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Affiliation(s)
- Marcus W. Beck
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
- Tampa Bay Estuary Program, Saint Petersburg, FL, USA
| | - Casey O’Hara
- Bren School of Environmental Sciences & Management, University of California, Santa Barbara, CA, USA
| | | | - Raphael D. Mazor
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - David J. Gillett
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Belize Lane
- Department of Civil and Environmental Engineering, Utah Water Research Laboratory, Utah State University, Logan, UT, USA
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Abstract
With increasing demand for training in data science, extracurricular or "ad hoc" education efforts have emerged to help individuals acquire relevant skills and expertise. Although extracurricular efforts already exist for many computationally intensive disciplines, their support of data science education has significantly helped in coping with the speed of innovation in data science practice and formal curricula. While the proliferation of ad hoc efforts is an indication of their popularity, less has been documented about the needs that they are designed to meet, the limitations that they face, and practical suggestions for holding successful efforts. To holistically understand the role of different ad hoc formats for data science, we surveyed organizers of ad hoc data science education efforts to understand how organizers perceived the events to have gone-including areas of strength and areas requiring growth. We also gathered recommendations from these past events for future organizers. Our results suggest that the perceived benefits of ad hoc efforts go beyond developing technical skills and may provide continued benefit in conjunction with formal curricula, which warrants further investigation. As increasing numbers of researchers from computational fields with a history of complex data become involved with ad hoc efforts to share their skills, the lessons learned that we extract from the surveys will provide concrete suggestions for the practitioner-leaders interested in creating, improving, and sustaining future efforts.
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Affiliation(s)
- Orianna DeMasi
- Department of Computer Science, University of California, Davis, California, United States of America
| | - Alexandra Paxton
- Department of Psychological Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- Center for the Ecological Study of Perception and Action, University of Connecticut, Storrs, Connecticut, United States of America
| | - Kevin Koy
- IDEO, San Francisco, California, United States of America
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Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Res 2019; 8. [PMID: 33163154 PMCID: PMC7607484 DOI: 10.12688/f1000research.20244.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 12/25/2022] Open
Abstract
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Bérénice Batut
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Peter Belmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Frank Oliver Glöckner
- Alfred-Wegener-Institut - Helmholtz Zentrum für Polar- und Meeresforschung and Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, 44227, Germany
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - René Rahn
- Algorithmic Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustraße 9, Berlin, 14195, Germany
| | - Maja Rey
- Scientific Databases and Visualization Group, Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - Malvika Sharan
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Ulrike Trojahn
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Björn Usadel
- IBG-2 Plant Sciences, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72076, Germany.,Translational Bioinformatics, University Hospital Tubingen, Tübingen, 72076, Germany.,Biomolecular Interactions, Max Planck Institute for Development Biology, Tübingen, 72076, Germany
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