Title

A Training Module to Introduce Undergraduate Students the Analytical Pipelines for Omics Data in Biomedical Research

Description/Abstract/Artist Statement

High throughput sequencing techniques bring the opportunity to profile various of cellular activities at the whole-genome level, such as RNA-seq for gene expression, ATAC-seq for chromatin accessibility and WGBS for DNA methylation. The value of the raw data produced by the sequencing equipment in advancing our understanding of important cellular biological processes relies on computational tools that can efficiently preprocess and make sense the data. Given the very large size of omics datasets, both advanced computational techniques and high-performance computing resources need to be utilized. Therefore, to successfully carry out such research, both good understanding of related biological concepts and skills for making use of the computing resources are critical. Here, we present a training module that we developed to introduce analytical pipelines for omics data, aiming at training undergraduate students with diversity background and promoting their interest in carrying out biomedical research in their future study. Three pipelines are covered in our module for processing three distinct types of omics data, respectively, i.e., transcriptomics, whole-genome chromatin accessibility and DNA methylomics. Brief introduction of related biologic concepts is included for training students without biological background. Quizzes are provided at the end of the module to evaluate the students’ understanding of the introduced concepts. In addition, programming exercises of running the pipelines on sample omics datasets were developed for students to gain hands on experience. We will deploy this learning module on a server and make it available to all students at ODU.

Presenting Author Name/s

Sean Leonard

Faculty Advisor/Mentor

Jiangwen Sun

College Affiliation

College of Sciences

Presentation Type

Poster

Disciplines

Other Computer Sciences

Session Title

Computer Science and its Impact in Science and Engineering

Location

Zoom Room S

Start Date

3-20-2021 12:00 PM

End Date

3-20-2021 12:55 PM

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Mar 20th, 12:00 PM Mar 20th, 12:55 PM

A Training Module to Introduce Undergraduate Students the Analytical Pipelines for Omics Data in Biomedical Research

Zoom Room S

High throughput sequencing techniques bring the opportunity to profile various of cellular activities at the whole-genome level, such as RNA-seq for gene expression, ATAC-seq for chromatin accessibility and WGBS for DNA methylation. The value of the raw data produced by the sequencing equipment in advancing our understanding of important cellular biological processes relies on computational tools that can efficiently preprocess and make sense the data. Given the very large size of omics datasets, both advanced computational techniques and high-performance computing resources need to be utilized. Therefore, to successfully carry out such research, both good understanding of related biological concepts and skills for making use of the computing resources are critical. Here, we present a training module that we developed to introduce analytical pipelines for omics data, aiming at training undergraduate students with diversity background and promoting their interest in carrying out biomedical research in their future study. Three pipelines are covered in our module for processing three distinct types of omics data, respectively, i.e., transcriptomics, whole-genome chromatin accessibility and DNA methylomics. Brief introduction of related biologic concepts is included for training students without biological background. Quizzes are provided at the end of the module to evaluate the students’ understanding of the introduced concepts. In addition, programming exercises of running the pipelines on sample omics datasets were developed for students to gain hands on experience. We will deploy this learning module on a server and make it available to all students at ODU.