1
|
Poulain P, Bertrand M, Dufour H, Taly A. A field guide for implementing a flipped classroom. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:410-417. [PMID: 37148479 DOI: 10.1002/bmb.21737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/07/2023] [Indexed: 05/08/2023]
Abstract
The way flipped classrooms are perceived and even practiced by teachers is sometimes approximate. For instance, while the Covid-19 pandemic has pushed many universities to adopt distance learning, flipped classrooms have often been mentioned as a solution in that context. This inducement maintains a confusion between flipped classrooms and distance learning that might be detrimental for students and teachers. Moreover, embarking on a new pedagogical practice such as flipped classroom could be intimidating and time-consuming for the newcomer teacher. For these reasons, this article aims to share some tips for implementing a flipped classroom, with examples from biology and biochemistry. Based on our experiences but also on the current scientific literature, we structured these advise around three phases: preparation, implementation, and follow-up. In the preparation phase, we advise planning early to invert time in class and outside the classroom, but also to say it explicitly, as well as to identify (or optionally create) resources for students to learn in autonomy. In the implementation phase, we suggest to (i) be explicit in the acquisition of knowledge and foster students' autonomy; (ii) explore active learning in class; (iii) develop cooperation and sharing skills; and (iv) differentiate teaching practices to adapt to student needs. Lastly, in the follow-up phase, we propose to (i) evaluate both student learning and the pedagogical setting; (ii) take care of the logistics and the teacher's posture; (iii) document the flipped classroom, and (iv) share the teaching experience.
Collapse
Affiliation(s)
- Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Mickael Bertrand
- Lycée Anna Judic, Éducation Nationale, Académie de Dijon, Semur-en-Auxois, France
| | | | - Antoine Taly
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
| |
Collapse
|
2
|
Couvin D, Dereeper A, Meyer DF, Noroy C, Gaete S, Bhakkan B, Poullet N, Gaspard S, Bezault E, Marcelino I, Pruneau L, Segretier W, Stattner E, Cazenave D, Garnier M, Pot M, Tressières B, Deloumeaux J, Breurec S, Ferdinand S, Gonzalez-Rizzo S, Reynaud Y. KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies). BIOINFORMATICS ADVANCES 2022; 2:vbac010. [PMID: 36699379 PMCID: PMC9710593 DOI: 10.1093/bioadv/vbac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 01/28/2023]
Abstract
Summary Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact dcouvin@pasteur-guadeloupe.fr. Supplementary information Supplementary data are available at Bioinformatics Advances online.
Collapse
Affiliation(s)
- David Couvin
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,To whom correspondence should be addressed
| | - Alexis Dereeper
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Damien F Meyer
- CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe 97170, France,ASTRE, Univ Montpellier, CIRAD, INRAE, Montpellier 34000, France
| | - Christophe Noroy
- Développement, Analyse, Transfert et Application (DATA), Lamentin, Guadeloupe 97129, France
| | - Stanie Gaete
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Bernard Bhakkan
- Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Nausicaa Poullet
- URZ Recherches Zootechniques, INRAE, Petit-Bourg, Guadeloupe 97170, France
| | - Sarra Gaspard
- Laboratoire COVACHIMM2E EA3592, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Etienne Bezault
- UMR BOREA (MNHN, CNRS-7208, IRD-207, Sorbonne Université, UCN, UA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Isabel Marcelino
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Ludovic Pruneau
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Wilfried Segretier
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Erick Stattner
- Laboratoire de Mathématiques Informatique et Applications (LAMIA), Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Damien Cazenave
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Maëlle Garnier
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Matthieu Pot
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Benoît Tressières
- Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Jacqueline Deloumeaux
- Karubiotec Centre de Ressources Biologiques-UF 0216, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France,Registre des cancers de Guadeloupe, CHU de la Guadeloupe, Pointe-à-Pitre 97110, France
| | - Sébastien Breurec
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France,Centre d’Investigation Clinique Antilles Guyane, Inserm CIC 1424, Les Abymes, Pointe-à-Pitre, Guadeloupe 97110, France,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Séverine Ferdinand
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| | - Silvina Gonzalez-Rizzo
- Équipe « Biologie de la mangrove » UMR7205 « ISYEB » MNHN-CNRS-Sorbonne Université-EPHE-UA, UFR SEN Département de Biologie, Université des Antilles, Pointe-à-Pitre, Guadeloupe 97110, France
| | - Yann Reynaud
- Unité Transmission, Réservoir et Diversité des Pathogènes, Institut Pasteur de Guadeloupe, Les Abymes, Guadeloupe 97139, France
| |
Collapse
|
3
|
Blasco A, Endres MG, Sergeev RA, Jonchhe A, Macaluso NJM, Narayan R, Natoli T, Paik JH, Briney B, Wu C, Su AI, Subramanian A, Lakhani KR. Advancing computational biology and bioinformatics research through open innovation competitions. PLoS One 2019; 14:e0222165. [PMID: 31560691 PMCID: PMC6764653 DOI: 10.1371/journal.pone.0222165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/22/2019] [Indexed: 11/19/2022] Open
Abstract
Open data science and algorithm development competitions offer a unique avenue for rapid discovery of better computational strategies. We highlight three examples in computational biology and bioinformatics research in which the use of competitions has yielded significant performance gains over established algorithms. These include algorithms for antibody clustering, imputing gene expression data, and querying the Connectivity Map (CMap). Performance gains are evaluated quantitatively using realistic, albeit sanitized, data sets. The solutions produced through these competitions are then examined with respect to their utility and the prospects for implementation in the field. We present the decision process and competition design considerations that lead to these successful outcomes as a model for researchers who want to use competitions and non-domain crowds as collaborators to further their research.
Collapse
Affiliation(s)
- Andrea Blasco
- Laboratory for Innovation Science at Harvard, Harvard University, Cambridge, MA, United States of America
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, United States of America
- The Broad Institute, Cambridge, MA, United States of America
- * E-mail:
| | - Michael G. Endres
- Laboratory for Innovation Science at Harvard, Harvard University, Cambridge, MA, United States of America
- Institute for Quantitative Social Science, Harvard University, Cambridge, MA, United States of America
| | - Rinat A. Sergeev
- Laboratory for Innovation Science at Harvard, Harvard University, Cambridge, MA, United States of America
- Harvard Business School, Harvard University, Boston, MA, United States of America
| | - Anup Jonchhe
- The Broad Institute, Cambridge, MA, United States of America
| | | | - Rajiv Narayan
- The Broad Institute, Cambridge, MA, United States of America
| | - Ted Natoli
- The Broad Institute, Cambridge, MA, United States of America
| | - Jin H. Paik
- Laboratory for Innovation Science at Harvard, Harvard University, Cambridge, MA, United States of America
- Harvard Business School, Harvard University, Boston, MA, United States of America
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | | | - Karim R. Lakhani
- Laboratory for Innovation Science at Harvard, Harvard University, Cambridge, MA, United States of America
- Harvard Business School, Harvard University, Boston, MA, United States of America
- National Bureau of Economic Research, Cambridge, MA, United States of America
| |
Collapse
|
4
|
Zhan YA, Wray CG, Namburi S, Glantz ST, Laubenbacher R, Chuang JH. Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors. PLoS Comput Biol 2019; 15:e1007026. [PMID: 31194735 PMCID: PMC6563947 DOI: 10.1371/journal.pcbi.1007026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bioinformatics has become an indispensable part of life science over the past 2 decades. However, bioinformatics education is not well integrated at the undergraduate level, especially in liberal arts colleges and regional universities in the United States. One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area. Most current life science professors did not acquire bioinformatics analysis skills during their own training. Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education. To address this gap, we developed a module-based, week-long short course to train small college and regional university professors with essential bioinformatics skills. The bioinformatics modules were built to be adapted by the professor-trainees afterward and used in their own classes. All the course materials can be accessed at https://github.com/TheJacksonLaboratory/JAXBD2K-ShortCourse.
Collapse
Affiliation(s)
- Yingqian Ada Zhan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Charles Gregory Wray
- Genomic Education, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Spencer T. Glantz
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Reinhard Laubenbacher
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Center for Quantitative Medicine, UConn Health, Farmington, Connecticut, United States of America
| | - Jeffrey H. Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, United States of America
| |
Collapse
|