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Orchestrating a community-developed computational workshop and accompanying training materials
The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and an...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234736/ https://www.ncbi.nlm.nih.gov/pubmed/30473781 http://dx.doi.org/10.12688/f1000research.16516.1 |
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author | Davis, Sean Ramos, Marcel Shepherd, Lori Turaga, Nitesh Geistlinger, Ludwig Morgan, Martin T. Haibe-Kains, Benjamin Waldron, Levi |
author_facet | Davis, Sean Ramos, Marcel Shepherd, Lori Turaga, Nitesh Geistlinger, Ludwig Morgan, Martin T. Haibe-Kains, Benjamin Waldron, Levi |
author_sort | Davis, Sean |
collection | PubMed |
description | The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and analytical methods. Here, we detail the process we used to produce high-quality, community-authored educational materials that are available for public consumption and reuse. The coordinated efforts of 17 authors over 10 weeks resulted in 15 workshops available as a website and as a 388-page electronic book. We describe how we utilized cloud infrastructure, GitHub, and a literate programming approach to robustly deliver hands-on tutorials to participants of the annual Bioconductor conference. The scripts, raw and published workshop materials, and cloud machine image are all openly available. Our approach uses free services and software and can be adapted by workshop organizers and authors in other contests with appropriate technical backgrounds. |
format | Online Article Text |
id | pubmed-6234736 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-62347362018-11-23 Orchestrating a community-developed computational workshop and accompanying training materials Davis, Sean Ramos, Marcel Shepherd, Lori Turaga, Nitesh Geistlinger, Ludwig Morgan, Martin T. Haibe-Kains, Benjamin Waldron, Levi F1000Res Method Article The importance of bioinformatics, computational biology, and data science in biomedical research continues to grow, driving a need for effective instruction and education. A workshop setting, with lectures and guided hands-on tutorials, is a common approach to teaching practical computational and analytical methods. Here, we detail the process we used to produce high-quality, community-authored educational materials that are available for public consumption and reuse. The coordinated efforts of 17 authors over 10 weeks resulted in 15 workshops available as a website and as a 388-page electronic book. We describe how we utilized cloud infrastructure, GitHub, and a literate programming approach to robustly deliver hands-on tutorials to participants of the annual Bioconductor conference. The scripts, raw and published workshop materials, and cloud machine image are all openly available. Our approach uses free services and software and can be adapted by workshop organizers and authors in other contests with appropriate technical backgrounds. F1000 Research Limited 2018-10-17 /pmc/articles/PMC6234736/ /pubmed/30473781 http://dx.doi.org/10.12688/f1000research.16516.1 Text en Copyright: © 2018 Davis S et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The author(s) is/are employees of the US Government and therefore domestic copyright protection in USA does not apply to this work. The work may be protected under the copyright laws of other jurisdictions when used in those jurisdictions. |
spellingShingle | Method Article Davis, Sean Ramos, Marcel Shepherd, Lori Turaga, Nitesh Geistlinger, Ludwig Morgan, Martin T. Haibe-Kains, Benjamin Waldron, Levi Orchestrating a community-developed computational workshop and accompanying training materials |
title | Orchestrating a community-developed computational workshop and accompanying training materials |
title_full | Orchestrating a community-developed computational workshop and accompanying training materials |
title_fullStr | Orchestrating a community-developed computational workshop and accompanying training materials |
title_full_unstemmed | Orchestrating a community-developed computational workshop and accompanying training materials |
title_short | Orchestrating a community-developed computational workshop and accompanying training materials |
title_sort | orchestrating a community-developed computational workshop and accompanying training materials |
topic | Method Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234736/ https://www.ncbi.nlm.nih.gov/pubmed/30473781 http://dx.doi.org/10.12688/f1000research.16516.1 |
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