Contreras-Peruyero Haydeé, Guerrero-Flores Shaday, Zirión-Martínez Claudia, Mejía-Ponce Paulina M, Navarro-Miranda Marisol, Lovaco-Flores J Abel, Ibarra-Rodríguez José M, Pashkov Anton, Licona-Cassani Cuauhtémoc, Sélem-Mojica Nelly
Centro de Ciencias Matemáticas, UNAM, Antigua Carretera a Pátzcuaro # 8701, Residencial San José de la Huerta, Morelia, Michoacán 58089, Mexico.
School of Engineering and Sciences, Tecnológico de Monterrey, Monterrey 64849, Mexico.
Bioinform Adv. 2024 Sep 27;4(1):vbae139. doi: 10.1093/bioadv/vbae139. eCollection 2024.
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.
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.
https://carpentries-incubator.github.io/pangenomics-workshop/.
随着基因组数据分析变得越来越复杂，研究人员面临着掌握各种软件工具的挑战。泛基因组学分析的兴起，即对一组基因组中的全套基因进行研究，在理解遗传多样性方面具有特别的变革性。我们由生物学家和数学家组成的跨学科团队开发了一个简短的泛基因组学研讨会，内容涵盖Bash、Python脚本、泛基因组和拓扑数据分析。这些技能为深入了解遗传变异及其在进化生物学中的意义提供了帮助。该研讨会使用Conda环境以实现可重复性和可访问性。该研讨会在Carpentries孵化器基础设施中开发，旨在使研究人员具备泛基因组学研究的基本技能。通过强调实践社区的作用，这项工作强调了其在使多学科专业人员能够协作开发遵循最佳实践的培训方面的重要性。
我们的研讨会通过提升计算生物学专业人员的技能集带来了切实的成果。参与者通过使用来自首次描述的泛基因组的真实数据获得了实践经验。我们分享了创建一个开源、多学科和公共资源的过程，学习者可以在其中发展泛基因组分析方面的专业知识。这一举措不仅提升了个人能力，还符合满足计算生物学教育需求这一更广泛的使命。
https://carpentries-incubator.github.io/pangenomics-workshop/ 。
