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Online Tools for Teaching Cancer Bioinformatics
The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442005/ https://www.ncbi.nlm.nih.gov/pubmed/34594439 http://dx.doi.org/10.1128/jmbe.00167-21 |
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author | Taylor, Mason D. Mendenhall, Bryn Woods, Calvin S. Rasband, Madeline E. Vallejo, Milene C. Bailey, Elizabeth G. Payne, Samuel H. |
author_facet | Taylor, Mason D. Mendenhall, Bryn Woods, Calvin S. Rasband, Madeline E. Vallejo, Milene C. Bailey, Elizabeth G. Payne, Samuel H. |
author_sort | Taylor, Mason D. |
collection | PubMed |
description | The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore biological phenomena with computational tools, including data manipulation, visualization, and statistical assessment. However, logistical barriers to data access and integration often complicate their use in undergraduate education. Here, we present a cancer bioinformatics module that is designed to overcome these barriers through six exercises containing authentic, biologically motivated computational exercises that demonstrate how modern omics data are used in precision oncology. Upper-division undergraduate students develop advanced Python programming and data analysis skills with real-world oncology data which integrates proteomics and genomics. The module is publicly available and open source at https://paynelab.github.io/biograder/bio462. These hands-on activities include explanatory text, code demonstrations, and practice problems and are ready to implement in bioinformatics courses. |
format | Online Article Text |
id | pubmed-8442005 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-84420052021-09-29 Online Tools for Teaching Cancer Bioinformatics Taylor, Mason D. Mendenhall, Bryn Woods, Calvin S. Rasband, Madeline E. Vallejo, Milene C. Bailey, Elizabeth G. Payne, Samuel H. J Microbiol Biol Educ Tips and Tools The rise of deep molecular characterization with omics data as a standard in biological sciences has highlighted a need for expanded instruction in bioinformatics curricula. Many large biology data sets are publicly available and offer an incredible opportunity for educators to help students explore biological phenomena with computational tools, including data manipulation, visualization, and statistical assessment. However, logistical barriers to data access and integration often complicate their use in undergraduate education. Here, we present a cancer bioinformatics module that is designed to overcome these barriers through six exercises containing authentic, biologically motivated computational exercises that demonstrate how modern omics data are used in precision oncology. Upper-division undergraduate students develop advanced Python programming and data analysis skills with real-world oncology data which integrates proteomics and genomics. The module is publicly available and open source at https://paynelab.github.io/biograder/bio462. These hands-on activities include explanatory text, code demonstrations, and practice problems and are ready to implement in bioinformatics courses. American Society for Microbiology 2021-08-31 /pmc/articles/PMC8442005/ /pubmed/34594439 http://dx.doi.org/10.1128/jmbe.00167-21 Text en Copyright © 2021 Taylor et al. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | Tips and Tools Taylor, Mason D. Mendenhall, Bryn Woods, Calvin S. Rasband, Madeline E. Vallejo, Milene C. Bailey, Elizabeth G. Payne, Samuel H. Online Tools for Teaching Cancer Bioinformatics |
title | Online Tools for Teaching Cancer Bioinformatics |
title_full | Online Tools for Teaching Cancer Bioinformatics |
title_fullStr | Online Tools for Teaching Cancer Bioinformatics |
title_full_unstemmed | Online Tools for Teaching Cancer Bioinformatics |
title_short | Online Tools for Teaching Cancer Bioinformatics |
title_sort | online tools for teaching cancer bioinformatics |
topic | Tips and Tools |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8442005/ https://www.ncbi.nlm.nih.gov/pubmed/34594439 http://dx.doi.org/10.1128/jmbe.00167-21 |
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