Using Basic Command Lines in Undergraduate Genomics Classes
Linux-based software systems remain the primary tools used for many elements of genome-scale research, yet undergraduates rarely receive any introduction or training related to these important and burgeoning topics in biology. This workshop will introduce the importance and utility of Linux command line approaches in genome-scale research using locally or nationally available high performance computing systems. This workshop will cover the incorporation of Linux tools into an undergraduate genomics course focusing on a variety topics, including elements of experimental design, data quality assessment for next generation sequencing data, the assembly of genomes and transcriptomes, the annotation of genomes, the characterization of genomes and associated comparative analyses.
- The importance of next generation sequencing technology in genomics research
- The utility of Linux tools and high performance computing systems for handling next generation sequencing data
- The flexibility and power of the open source Linux platform in genome biology.
- Lab exercises developed for a such a course can be used to teach students about genome assembly and annotation, transcriptome analysis, and comparative analyses.
Donovan’s undergraduate, graduate, postdoctoral and continued training have focused on the use of molecular biology tools (mostly DNA-based) to address a broad range of questions in comparative evolutionary biology of plants. His “traditional” background in morphology and evolution in combination with training in molecular biology provides strong educational opportunities for students in the lab and classroom. In recent years, he has worked to expand opportunities for student training in areas related to “next generation sequencing” and large data set bioinformatics through the development of courses/experiences that provide students with a background in large dataset bioinformatics as critical skills in modern biology.
Workshop Sponsors and External Links
October 14, 2022
- Tammy Castro – Professor of Biology, Bloomfield College
- Nate Jue – Associate Professor, California State University, Monterey Bay
- Justine Garcia – Assistant Professor of Biology, New Mexico Highlands University
- David Torres – Chair of Mathematics and Physical Science, Northern New Mexico College
- Dimah Dera – Assistant Professor of Biology, University of Texas Rio Grande Valley
- Eric Garcia – Postdoc & Research Manager, Old Dominion University
- Sridhar Malkaram – Associate Professor, West Virginia State University
- Supratik Kar – Assistant Professor, Kean University
- Nabarun Ghosh – Professor, West Texas A&M University