Bioinformatics Bootcamp: A model for training clinical researchers
Main Article Content
Abstract
Within the last few decades, there has been a steady decline in physicians conducting research. The U.S. biomedical workforce is aging which affects improving health care in this country. As they age, we need innovative ways to increase the physician-scientist pool. Along with shortages of under-represented minorities in this field, there is a scarcity of people able to analyze biological data. In an effort to increase the number of under-represented minorities conducting bioinformatics/genomics research, the Human Genome Sequencing Center-Genetics/Genomics Research Education Training (G/GREAT) program created a bioinformatics mini course. The Bioinformatics Bootcamp course offers an opportunity to learn a skill that will increase summer interns’ self-confidence, interest, and proficiency in seeking future computational research opportunities. This study will determine the best training approach to accomplish this goal for the novice (non-experienced) student. We surveyed course instructors to understand their bioinformatics teaching method and G/GREAT interns for their perspectives concerning the course. The results provided value information that guided curriculum design for all future G/GREAT training courses. These outcomes suggest that similar courses aimed at clinicians interested in research could increase physician scientists to begin replacing those about to retire.
Terms: Interns=students=participants, programming=coding, non-experienced=novice.
Keywords:
interns, students, participants, programming, coding, non-experienced, novice
Article Details
How to Cite
MURRAY, Debra et al.
Bioinformatics Bootcamp: A model for training clinical researchers.
Medical Research Archives, [S.l.], v. 8, n. 5, may 2020.
ISSN 2375-1924.
Available at: <https://esmed.org/MRA/mra/article/view/2108>. Date accessed: 22 dec. 2024.
doi: https://doi.org/10.18103/mra.v8i5.2108.
Section
Research Articles
The Medical Research Archives grants authors the right to publish and reproduce the unrevised contribution in whole or in part at any time and in any form for any scholarly non-commercial purpose with the condition that all publications of the contribution include a full citation to the journal as published by the Medical Research Archives.
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2. AAMC. Is an MD-PhD Right for Me? https://students-residents.aamc.org/choosing-medical-career/article/md-phd-right-for-me/. Access March 7, 2020.
3. Kaiser, J. NIH report warns of looming shortage of physician-scientist. Science. https://www.sciencemag.org/news/2014/06/nih-report-warns-looming-shortage-physician-scientists#. Published June 9, 2014. Accessed March 15, 2020.
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7. Kemper, AR, Trotter, TL, Lloyd-Puryear, MA, Kyler, P, Feero, WG, Howell, RR. A blueprint for maternal and child health primary care physician education in medical genetics and genomics medicine: Recommendations of the United State Secretary of Health and Human Services Advisory Committee on Heritable Disorders in newborns and Children. Genetics in Medicine. 2009; 12 (2): 77-80.
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https://doi.org/10.1172/JCI34772
13. National Institutes of Health All of Us Research Program. The future of health begins with you. https://allofus.nih.gov/
14. Sudmant, P., Rausch, T., Gardner, E., ….Korbel, J. An integrated map of structural variation in 2,504 human genomes Nature. 2015. vol 526: 75-81. doi:10.1038/nature15394
15. Chang, J. Core services: reward bioinformaticians. Nature. 2015. 520 (7546), 151-152. doi:10.1038/520151a
16. Revolutionizing Science and Engineering Through Cyberinfrastructure: Report on the National Science Foundation Blue Ribbon Advisory Panel on Cyberinfrastructure (whitepaper). 2003 Advisory Panel on Cyberinfrastructure. www.cise.nsf.gov/sci/reports/atkins.pdf
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18. Mendez, R., Torres, J., Ishwad, P., Nicholas, H., and Ropelewski, A. Assisting bioinformatics programs at minority institutions: needs assessment, and lessons learned-a look at an internship program. http://dx.doi.org/10.1145/2949550.2949641
19. Anupama, J., Francescatto, M., Rahman, F., Fatima, N., DeBiasio, D., Shanmugam, A., Satagopam, v., Santos, A., Kolekar, P., Michaut, M., and Guney, E. The ISCB Student Council Internship Program: Expanding computational biology capacity worldwide. PLos Comput Biol 2018; 14 (1): e1005802. https://doi.org/10.1371/journal.pcbi.1005802
20. Wang, T. Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support. FEMS Microbiology Letters 2017;364 (15): 1-9. Doi: 10.1093/femsle/fns157
21. Tambi, R., Bayoumi, R., Lansberg, P., Banerjee, Y. Blending Gagne’s Instructional Model with Peyton’s Approach to desgn an introductory bioinformatics lesson plan for medical students: proof-of-concept study. JMIR Med Educ 2018; 4 (2). doi: 10.2196/11122
22. Goode, E., and Trajkovski, G. Developing a truly interdisciplinary bioinformatics track: work in progress. JCSC 22, 6 (June 2007).
23. Hemminger, B., Losi, T., and Bauers, A., (2005) Survey of Bioinformatics programs in the United States. J American Society for Information Science and Technology, 56 (5): 529-537.
24. Shaffer, J., Mather, F., Wele, M., Li, J., Tangara, C., Kassogue, Y., Srivastav, S., Thiero, O., Diakite, M., Sangare, M., Dabitao, D., Toure, M., Djimde, A., Traore, S., Kiakite, B., Coulibaly, M., Liu, Y., Lacey, M., Lefante, J., Koita, O., Schieffelin, J., Krogstad, D., and Doumbia, S. Expanding Research Capacity in Sub-Saharan Africa Through Informatics, Bioinformatics, and Data Science Training Programs, in Mali. Frontiers in Genetics 2019; 10 (331): 1-13. doi: 10.3389/fgene.2019.00331
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26. Fatumo, S., Adoga, M., Ojo, O., Oluwagbemi, O., Adeoye, T., Ewejobi, I., Adebiyi, M., Adebiyi, E., Bewaji, C., and Nashiru, O. Computational biology and bioinformatics in Nigeria. PLoS Computational Biology. 2014; 10 (4): e1003516. doi:10.1371/journal.pcbi.1003516
27. Bishop, O., Adebiyi, E., Alzohairy, Al, Everett, D., Ghedira, K., Ghouila, A., Kumuthini, J., Mulder, N., Panji, S., and Patterton, H. Bioinformatics Education-perspectives and challenges out of Africa. Briefings in Bioinformatics 2014; 16 (2): 355-364. doi: 10.1093/bib/bbu022
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29. Dong, T., Durning, S., Gilliland, W., Waechter, D., Cruess, D., DeZee, K., Calloway, M., Artino, A. Exploring the relationship between self-reported research experience and performance in medical school and internship. Military Medicine 2012; 177, 9:11.
30. Zeng, W., Woodhouse, R., and Brunt, M. Do preclinical background and clerkship experiences impact skills performance in an accelerated internship preparation course for senior medical students? Surgery 2010; 148 (4); 768-777. doi:10.1016/j.surg.2010.07.022
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32. Kemper, A., Trotter, T., Lloyd-Puryear, M., Kyler, P., Feero, W., and Howell, R. A blueprint for maternal and child health primary care physician education in medical genetics and genomic medicine: Recommendations of the United States Secretary for Health and Human Services Advisory committee on heritable Disorders in Newborns and children. Genetics in Medicine 2010; 12(2): 77-80.