Meeting the challenge of genomic analysis: a collaboratively developed workshop for pangenomics and topological data analysis
Por:
Contreras-Peruyero H., Guerrero-Flores S., Zirión-Martínez C., Mejía-Ponce P.M., Navarro-Miranda M., Lovaco-Flores J.A., Ibarra-Rodríguez J.M., Pashkov A., Licona-Cassani C., Sélem-Mojica N.
Publicada:
1 ene 2024
Resumen:
Motivation: As genomics data analysis becomes increasingly intricate, researchers face the challenge of mastering various software tools. The rise of Pangenomics analysis, which examines the complete set of genes in a group of genomes, is particularly transformative in understanding genetic diversity. Our interdisciplinary team of biologists and mathematicians developed a short Pangenomics Workshop covering Bash, Python scripting, Pangenome, and Topological Data Analysis. These skills provide deeper insights into genetic variations and their implications in Evolutionary Biology. The workshop uses a Conda environment for reproducibility and accessibility. Developed in The Carpentries Incubator infrastructure, the workshop aims to equip researchers with essential skills for Pangenomics research. By emphasizing the role of a community of practice, this work underscores its significance in empowering multidisciplinary professionals to collaboratively develop training that adheres to best practices. Results: Our workshop delivers tangible outcomes by enhancing the skill sets of Computational Biology professionals. Participants gain hands-on experience using real data from the first described pangenome. We share our paths toward creating an open-source, multidisciplinary, and public resource where learners can develop expertise in Pangenomic Analysis. This initiative goes beyond advancing individual capabilities, aligning with the broader mission of addressing educational needs in Computational Biology. © 2024 The Author(s). Published by Oxford University Press.
Filiaciones:
Contreras-Peruyero H.:
Centro de Ciencias Matemáticas, UNAM, Antigua Carretera a Pátzcuaro # 8701, Residencial San Joséde la Huerta, Michoacán, Morelia, 58089, Mexico
Guerrero-Flores S.:
Centro de Ciencias Matemáticas, UNAM, Antigua Carretera a Pátzcuaro # 8701, Residencial San Joséde la Huerta, Michoacán, Morelia, 58089, Mexico
Zirión-Martínez C.:
School of Engineering and Sciences, Tecnológico de Monterrey, Monterrey, 64849, Mexico
Biology Department, Duke University, Durham, 27708, NC, United States
Mejía-Ponce P.M.:
School of Engineering and Sciences, Tecnológico de Monterrey, Monterrey, 64849, Mexico
Navarro-Miranda M.:
Genetic Engineering, Research and Advanced Studies Center (CINVESTAV-Irapuato), Irapuato, 36824, Mexico
Lovaco-Flores J.A.:
Genetic Engineering, Research and Advanced Studies Center (CINVESTAV-Irapuato), Irapuato, 36824, Mexico
Ibarra-Rodríguez J.M.:
C3 Idea, Guanajuato, León, 37500, Mexico
Pashkov A.:
National School of Higher Studies Morelia, UNAM, Morelia, 58089, Mexico
Licona-Cassani C.:
School of Engineering and Sciences, Tecnológico de Monterrey, Monterrey, 64849, Mexico
Sélem-Mojica N.:
Centro de Ciencias Matemáticas, UNAM, Antigua Carretera a Pátzcuaro # 8701, Residencial San Joséde la Huerta, Michoacán, Morelia, 58089, Mexico
gold, All Open Access; Gold Open Access
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