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Zuvanov L, Basso Garcia AL, Correr FH, Bizarria R, Filho APDC, da Costa AH, Thomaz AT, Pinheiro ALM, Riaño-Pachón DM, Winck FV, Esteves FG, Margarido GRA, Casagrande GMS, Frajacomo HC, Martins L, Cavalheiro MF, Grachet NG, da Silva RGC, Cerri R, Ramos RTJ, de Medeiros SDS, Tavares TV, Corrêa dos Santos RA. The experience of teaching introductory programming skills to bioscientists in Brazil. PLoS Comput Biol 2021; 17:e1009534. [PMID: 34762646 PMCID: PMC8584955 DOI: 10.1371/journal.pcbi.1009534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.
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Affiliation(s)
- Luíza Zuvanov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University, Rio Claro, Brazil
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | - Andréa T. Thomaz
- School of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Ana Lucia Mendes Pinheiro
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Flavia Vischi Winck
- Regulatory Systems Biology Lab, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Franciele Grego Esteves
- Center of the Study of Social Insects, Department of General and Applied Biology, Institute of Biosciences of Rio Claro, São Paulo State University, Rio Claro, Brazil
| | | | | | | | - Leonardo Martins
- Paulista School of Medicine, Federal University of São Paulo, São Paulo, Brazil
| | - Mariana Feitosa Cavalheiro
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Genomics for Climate Change Research Center, University of Campinas, Campinas, Brazil
| | | | - Raniere Gaia Costa da Silva
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, Special Administrative Region, People’s Republic of China
| | - Ricardo Cerri
- Department of Computer Science, Federal University of São Carlos, São Carlos, Brazil
| | | | | | - Thayana Vieira Tavares
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Renato Augusto Corrêa dos Santos
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, Brazil
- Institute of Biology, State University of Campinas, Campinas, Brazil
- * E-mail:
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Donald CL, Brennan B, Cumberworth SL, Rezelj VV, Clark JJ, Cordeiro MT, Freitas de Oliveira França R, Pena LJ, Wilkie GS, Da Silva Filipe A, Davis C, Hughes J, Varjak M, Selinger M, Zuvanov L, Owsianka AM, Patel AH, McLauchlan J, Lindenbach BD, Fall G, Sall AA, Biek R, Rehwinkel J, Schnettler E, Kohl A. Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil. PLoS Negl Trop Dis 2016; 10:e0005048. [PMID: 27706161 PMCID: PMC5051680 DOI: 10.1371/journal.pntd.0005048] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/19/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. METHODOLOGY/PRINCIPAL FINDINGS We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. CONCLUSIONS/SIGNIFICANCE The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions.
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Affiliation(s)
- Claire L. Donald
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Benjamin Brennan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | | | - Veronica V. Rezelj
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Jordan J. Clark
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Marli T. Cordeiro
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Rafael Freitas de Oliveira França
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Lindomar J. Pena
- Fundação Oswaldo Cruz-PE/Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Campus da UFPE-Cidade Universitária, Recife/PE, Brasil
| | - Gavin S. Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Christopher Davis
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Margus Varjak
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic
| | - Luíza Zuvanov
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Ania M. Owsianka
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Brett D. Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
| | - Gamou Fall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou A. Sall
- Pole de Virologie, Unité des arbovirus et virus des fièvres hémorragiques, Institut Pasteur de Dakar, Dakar, Senegal
| | - Roman Biek
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine and Radcliffe Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Esther Schnettler
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom
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