Empowering beginners in bioinformatics with ChatGPT

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

References

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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

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RIGHTS & PERMISSIONS

2023 The Author(s). Published by Higher Education Press.