Empowering beginners in bioinformatics with ChatGPT

Evelyn Shue, Li Liu, Bingxin Li, Zifeng Feng, Xin Li, Gangqing Hu

PDF(240 KB)
PDF(240 KB)
Quant. Biol. ›› 2023, Vol. 11 ›› Issue (2) : 105-108. DOI: 10.15302/J-QB-023-0327
PERSPECTIVE

Empowering beginners in bioinformatics with ChatGPT

Author information +
History +

Abstract

The impressive conversational and programming abilities of ChatGPT make it an attractive tool for facilitating the education of bioinformatics data analysis for beginners. In this study, we proposed an iterative model to fine-tune instructions for guiding a chatbot in generating code for bioinformatics data analysis tasks. We demonstrated the feasibility of the model by applying it to various bioinformatics topics. Additionally, we discussed practical considerations and limitations regarding the use of the model in chatbot-aided bioinformatics education.

Keywords

bioinformatics / education / scientific data analysis / ChatGPT

Cite this article

Download citation ▾
Evelyn Shue, Li Liu, Bingxin Li, Zifeng Feng, Xin Li, Gangqing Hu. Empowering beginners in bioinformatics with ChatGPT. Quant. Biol., 2023, 11(2): 105‒108 https://doi.org/10.15302/J-QB-023-0327

References

[1]
Chatterjee, J. (2023). This new conversational AI model can be your friend, philosopher, and guide... and even your worst enemy. Patterns, 4: 100676
CrossRef Google scholar
[2]
DurlachP. J.LesgoldA.. (2012) Adaptive Technologies for Training and Education. Cambridge: Cambridge University Press
[3]
The, ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489: 57–74
CrossRef Google scholar
[4]
ttir, H., Robinson, J. T. Mesirov, J. (2013). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform., 14: 178–192
CrossRef Google scholar
[5]
WeiJ.,WangX.,SchuurmansD.,BosmaM.,IhterB.,XiaF.,ChiE. H.,LeQ. V.. (2023) Chain of thought prompting elicits reasoning in large language models. In: 36th Conference on Neural Information Processing Systems (NeurIPS 2022)
[6]
Pavlik, J. (2023). Collaborating with chatgpt: Considering the implications of generative artificial intelligence for journalism and media education. Jour. Mass Comm. Educ., 78: 84–93
CrossRef Google scholar

SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.15302/J-QB-023-0327.
Fig. S1: The OPTIMAL model for LLM chatbot-assisted scientific data analysis; Fig. S2: Summary of case studies applying the OPTIMAL model to chatbot-assisted data analysis in five distinctive fields; Table S1: Case study for short sequencing reads alignment and visual inspection; Table S2: Case study for phylogeny inference by DNA sequences; Table S3: Case study for robust circles fitting; Table S4: Case study for household income vs. high school graduation rates; Table S5: Case study for time series analysis of trading data

ACKNOWLEDGEMENTS

NIH-NIGMS grants P20 GM103434, U54 GM-104942, and 1P20 GM121322 to GH; NIH-NLM grant R01LM013438 to LL. We thank Dr. Jackie J.D. Han from Peking University, Dr. Heather Henderson from West Virginia University, and Dr. Dong Xu from University of Missouri for insightful discussions. The writing was polished by ChatGPT.

COMPLIANCE WITH ETHICS GUIDELINES

Evelyn Shue, Li Liu, Bingxin Li, Zifeng Feng, Xin Li and Gangqing Hu declare that they have no conflict of interest.
This article is a perspective article and does not contain any studies with human or animal subjects performed by any of the authors.

OPEN ACCESS

This article is licensed by the CC By under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

RIGHTS & PERMISSIONS

2023 The Author(s). Published by Higher Education Press.
AI Summary AI Mindmap
PDF(240 KB)

Accesses

Citations

Detail

Sections
Recommended

/