Welcome to the FAIR Data Practices for Omics Analysis Workshop.
Technological advances in instrumentation for generating genomics, proteomics, and related data have made these high-throughput, data intensive technologies an indispensable part of biological research. Concurrent advances in computational infrastructure and data science methodologies have not only allowed analysis of these data for their original purpose, but have enabled subsequent reanalysis of such data by other investigators to meet other scientific objectives. This emerging paradigm has underscored the need for practices that make such data Findable, Accessible, Interoperable, and Reusable (FAIR). This workshop will provide primarily laboratory based scientists with the knowledge and tools they need to apply FAIR practices in their own research.
The FAIR Data Workshop held in April 2022 at UD was presented in the following order (materials are organized by day):
- Welcome and Workshop Overview
- Activity: Technology/Software orientation and test
- Lecture: Overview of FAIR data principles
- Activity: Good/bad data practice discussion
- Tutorial: Web-based resources
- Assignment: Web-based bioinformatics exercise
- Activity: Assignment report out
- Lecture: Computational notebooks
- Activity: Documenting computational work
- Lecture: Overview of omics analysis
- Tutorial: HPC and Biomix
- Assignment: Biomix exercise
- Lecture: Introduction to biomedical ontologies
- Lecture: Intro to SNP project
- Tutorial: Exploring NCBI SRA
- Activity: SRA dataset exploration
- Lecture: Environment ontology
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- Activity: SRA/ontology assignment
- Lecture: Genomic variants
- Lecture: Mis-annotations
- Lecture: Genomic Variant Analysis (SNP) Analysis
- Tutorial: SNP Tutorial 1: QC and trimming
- Lecture: Interoperability
- Tutorial: SNP Tutorial 2: Reference mapping & variant detection
- Assignment: Complete variant detection
- Tutorial: SNP Tutorial 3: Comparing variants
- Lecture: Iroki Overview
- Tutorial: SNP Tutorial 4: Viewing and decorating your tree
- Demonstration: Depositing sequence data in NCBI repositories
- Lecture: Other data repositories
- Lecture: Data usage licenses
Hosted by the UD Chemistry-Biology Interface Program and Center for Bioinformatics and Computational Biology. This workshop is offered free of charge with support from the NIH National Institute for General Medical Sciences (T32GM133395-03S1).
(c) 2022 by Shawn W. Polson and Amelia O. Harrison
The FAIR Data Practices for Omics Analysis workshop materials are licensed under a Creative Commons Attribution 4.0 International License.
You should have received a copy of the license along with this work. If not, see http://creativecommons.org/licenses/by/4.0/.