Literature DB >> 33630850

An integrated, modular approach to data science education in microbiology.

Kimberly A Dill-McFarland1,2, Stephan G König1,2, Florent Mazel1,2,3, David C Oliver1, Lisa M McEwen1,2,4, Kris Y Hong1,2, Steven J Hallam1,2,5,6,7.   

Abstract

We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.

Entities:  

Mesh:

Year:  2021        PMID: 33630850      PMCID: PMC7906378          DOI: 10.1371/journal.pcbi.1008661

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


  10 in total

1.  Swift action needed to close the skills gap in bioinformatics.

Authors:  M MacLean; C Miles
Journal:  Nature       Date:  1999-09-02       Impact factor: 49.962

2.  Active learning increases student performance in science, engineering, and mathematics.

Authors:  Scott Freeman; Sarah L Eddy; Miles McDonough; Michelle K Smith; Nnadozie Okoroafor; Hannah Jordt; Mary Pat Wenderoth
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-12       Impact factor: 11.205

Review 3.  The information science of microbial ecology.

Authors:  Aria S Hahn; Kishori M Konwar; Stilianos Louca; Niels W Hanson; Steven J Hallam
Journal:  Curr Opin Microbiol       Date:  2016-05-13       Impact factor: 7.934

4.  Null effects of boot camps and short-format training for PhD students in life sciences.

Authors:  David F Feldon; Soojeong Jeong; James Peugh; Josipa Roksa; Cathy Maahs-Fladung; Alok Shenoy; Michael Oliva
Journal:  Proc Natl Acad Sci U S A       Date:  2017-08-28       Impact factor: 11.205

Review 5.  A vision for collaborative training infrastructure for bioinformatics.

Authors:  Jason J Williams; Tracy K Teal
Journal:  Ann N Y Acad Sci       Date:  2016-09-07       Impact factor: 5.691

6.  Big Data: Astronomical or Genomical?

Authors:  Zachary D Stephens; Skylar Y Lee; Faraz Faghri; Roy H Campbell; Chengxiang Zhai; Miles J Efron; Ravishankar Iyer; Michael C Schatz; Saurabh Sinha; Gene E Robinson
Journal:  PLoS Biol       Date:  2015-07-07       Impact factor: 8.029

7.  A compendium of geochemical information from the Saanich Inlet water column.

Authors:  Mónica Torres-Beltrán; Alyse K Hawley; David Capelle; Elena Zaikova; David A Walsh; Andreas Mueller; Melanie Scofield; Chris Payne; Larysa Pakhomova; Sam Kheirandish; Jan Finke; Maya Bhatia; Olena Shevchuk; Esther A Gies; Diane Fairley; Céline Michiels; Curtis A Suttle; Frank Whitney; Sean A Crowe; Philippe D Tortell; Steven J Hallam
Journal:  Sci Data       Date:  2017-10-31       Impact factor: 6.444

8.  A compendium of multi-omic sequence information from the Saanich Inlet water column.

Authors:  Alyse K Hawley; Mónica Torres-Beltrán; Elena Zaikova; David A Walsh; Andreas Mueller; Melanie Scofield; Sam Kheirandish; Chris Payne; Larysa Pakhomova; Maya Bhatia; Olena Shevchuk; Esther A Gies; Diane Fairley; Stephanie A Malfatti; Angela D Norbeck; Heather M Brewer; Ljiljana Pasa-Tolic; Tijana Glavina Del Rio; Curtis A Suttle; Susannah Tringe; Steven J Hallam
Journal:  Sci Data       Date:  2017-10-31       Impact factor: 6.444

9.  A global perspective on evolving bioinformatics and data science training needs.

Authors:  Teresa K Attwood; Sarah Blackford; Michelle D Brazas; Angela Davies; Maria Victoria Schneider
Journal:  Brief Bioinform       Date:  2019-03-22       Impact factor: 11.622

10.  Power, pitfalls, and potential for integrating computational literacy into undergraduate ecology courses.

Authors:  Kaitlin J Farrell; Cayelan C Carey
Journal:  Ecol Evol       Date:  2018-07-30       Impact factor: 2.912

  10 in total

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