From high school to postdoc: Lessons from a decade of bioinformatics education

Presented at the Great Lakes Bioinformatics Conference in Chicago, IL as part of the Bioinformatics Education panel.

Transcript

1. From high school to postdoc: ! Lessons from a decade of bioinformatics education Mallory Freeberg Johns Hopkins University GLBIO – May 15, 2017
2. Outline •  Academic track •  Undergraduate/graduate education: strengths and weaknesses •  Components of successful bioinformatics education
3. The greatest adventure: the ballad of the bioinformatician •  High school Indiana, PA •  Saint Vincent College
 Latrobe, PA! BS Bioinformatics •  University of Michigan Ann Arbor, MI! PhD Bioinformatics •  Johns Hopkins University! Baltimore, MD! Postdoctoral research fellow u Academic track
4. Bioinformatics! What the heck is “bioinformatics”? u Academic track: High school Mathematics Biology + Computer science
5. Where can I get a bioinformatics degree? Bioinformatics undergraduate degree programs in Northeastern US in 2004: 3 u Academic track: Undergraduate collegeboard.org lists 49 US colleges that offer Bioinformatics undergraduate degrees (May 14, 2017)
6. Pioneering a bioinformatics BS degree at! Saint Vincent College (2005-2009) •  Core coursework + electives –  Biology/Chemistry (12) –  Computer/information science (7) –  Mathematics/biostatistics (2) –  Bioinformatics (2) •  Capstone research project •  External internships u Academic track: Undergraduate
7. Continuing bioinformatics education at the University of Michigan (2009-2015) •  Coursework –  Bioinformatics survey (1) –  Statistics/probability theory,! and mathematical modeling (4) –  Genomics/Transcriptomics (4) –  Data/Database systems (2) •  Rotations •  Bioinformatics journal club •  Annual progress reports u Academic track: Graduate In cohort of ~40 students, I was 1 of 2 with a bioinformatics BS degree
8. Continuing bioinformatics education at the University of Michigan (2009-2015) •  Additional training provided by thesis advisor –  Writing grants (R01s, graduate funding) –  Paper reviews –  Research presentations –  Collaborations u Academic track: Graduate
9. Preparing for a bioinformatics career at! Johns Hopkins University (2015-present) u Academic track: Postdoc undergraduate + graduate Teaching undergraduate + graduate Mentoring grade + middle school Outreach Research 2. The Galaxy Project (training/workshops + UI development) 1. Understanding post-transcriptional gene regulation with nanopore sequencing (experimental + computational)
10. Outline •  Academic track •  Undergraduate/graduate education: strengths and weaknesses •  Components of successful bioinformatics education
11. Undergraduate/graduate education:! strengths and weaknesses Strengths •  Exposure to variety of bioinformatics fields •  Research projects and internships early on •  Collaborations •  Career skill development (grants, reviews, etc.) Weaknesses •  Math/statistical theory •  Advanced computational skills (Big Data management, infrastructure) •  Cross-discipline training u Undergraduate/graduate: strengths and weaknesses
12. Outline •  Academic track •  Undergraduate/graduate education: strengths and weaknesses •  Components of successful bioinformatics education
13. Components of successful bioinformatics training •  Teach core competencies and their intersection •  Think “big data” •  Understand trainee’s end-goals –  Users – applying tools/algorithms/workflows –  Developers – developing tools/algorithms/workflows •  Foster appreciation for biological mechanisms, and concepts •  Start early! Especially exposure to a variety of fields and research environments
14. Acknowledgements •  Dr. Michael J. Bossé •  Dr. Michael L. Sierk •  Dr. John K. Kim •  Dr. James Taylor Thank you Questions?