| Literature DB >> 31194735 |
Yingqian Ada Zhan1, Charles Gregory Wray2, Sandeep Namburi1, Spencer T Glantz1, Reinhard Laubenbacher1,3, Jeffrey H Chuang1,4.
Abstract
Bioinformatics has become an indispensable part of life science over the past 2 decades. However, bioinformatics education is not well integrated at the undergraduate level, especially in liberal arts colleges and regional universities in the United States. One significant obstacle pointed out by the Network for Integrating Bioinformatics into Life Sciences Education is the lack of faculty in the bioinformatics area. Most current life science professors did not acquire bioinformatics analysis skills during their own training. Consequently, a great number of undergraduate and graduate students do not get the chance to learn bioinformatics or computational biology skills within a structured curriculum during their education. To address this gap, we developed a module-based, week-long short course to train small college and regional university professors with essential bioinformatics skills. The bioinformatics modules were built to be adapted by the professor-trainees afterward and used in their own classes. All the course materials can be accessed at https://github.com/TheJacksonLaboratory/JAXBD2K-ShortCourse.Entities:
Mesh:
Year: 2019 PMID: 31194735 PMCID: PMC6563947 DOI: 10.1371/journal.pcbi.1007026
Source DB: PubMed Journal: PLoS Comput Biol ISSN: 1553-734X Impact factor: 4.475
Program structure of Big Genomic Data Skills Training for Professors.
| Teaching Focus | Specific Topics | |
|---|---|---|
| JAX BD2K Program Structure | Basics | High-throughput sequencing technologies |
| Statistics | ||
| Scripting in R/UNIX | ||
| Modules | RNA-Seq | |
| Cancer variant | ||
| Exome | ||
| Microbiome | ||
| ChIP-Seq | ||
| Miscellaneous | Setting up educational cloud and grants | |
| Curriculum discussion | ||
| Slack discussion community |
Top, blue shade: Minimal cornerstones of bioinformatics introduced in the course.
Middle, orange shade: Modules on different data types covered by the 2018 course.
Bottom, green shade: Various topics to assist bioinformatics course development.
Abbreviations: BD2K, Big Data to Knowledge; ChIP, chromatin immunoprecipitation sequencing; JAX, The Jackson Laboratory; RNA-Seq, RNA sequencing.
Description of data analysis modules in Big Genomic Data Skills Training for Professors.
| Modules | Skills | Biology Question | Platform | Data Source |
|---|---|---|---|---|
| Differential gene expression analysis and gene set enrichment | What are genes affected by Pax6 knockout in male mice? | Galaxy | Mitchell and colleagues 2017 | |
| Data manipulation—grouping and sorting | What is the common driver mutation in three melanoma tumors? | Excel/R | Berger and colleagues 2012 | |
| Variant calling and filtering | Identify the exonic variant and gene responsible for the phenotype of “Leg dragger” | Galaxy | Fairfield and colleagues 2011 | |
| 16S analysis and bacterial taxon cataloging | What is the role of the microbiome in the development of type 1 diabetes in infants? | R/UNIX | ||
| Peak calling and motif analysis | Identify CTCF binding motif. | UNIX (Cloud) | ENCFF000ARV, ENCFF000ARP, ENCFF000ARK |
*“Leg dragger” is a spontaneous mutation leading to a phenotype where the mouse drags its rear legs and pulls it along with its front legs to move.
Abbreviations: ChIP-Seq, chromatin immunoprecipitation sequencing; RNA-Seq, RNA sequencing.
Fig 1Participant profile of Big Genomic Data Skills Training for Professors.
Background knowledge survey on 11 subjects. The expertise on each subject was evaluated from 1 (no knowledge) to 10 (expert). The mean score of each subject is shown at the right. The respondent ratio for each subject at every score is scaled to the center of each row and shown in color (middle panel). K-means clustering was conducted on the respondent ratio and presented to the left of the score matrix.
Fig 2Postevent survey on the satisfaction and evaluation of Big Genomic Data Skills Training for Professors.
(A) Participants’ overall satisfaction on the training program. (B) Distribution of degree of agreement on specific statements regarding the program. (C) Distribution of answers to their confidence to launch a course focused on genomics and genomics data analysis. (D) Distribution of participants’ willingness to implement our modules to their course. ChIP-Seq, chromatin immunoprecipitation sequencing; RNA-Seq, RNA sequencing.