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Code Interpreter for Bioinformatics: Are We There Yet?

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Annals of Biomedical Engineering Aims and scope Submit manuscript

Abstract

The Code Interpreter feature in ChatGPT has the potential to democratize data analysis for non-specialists. As bioinformaticians, we are impressed by its performance in data manipulation and visualization. However, bioinformatics tasks often require execution of third-party packages, access to annotation knowledgebase, and handling large datasets. Code Interpreter’s exclusive support for Python, no installation option for additional packages, inability to utilize external resources, and limited storage capacity could pose obstacles to its wide adoption in bioinformatics applications. To address these limitations, we advocated for the necessity of locally deployable, API-based systems for chatbot-aided bioinformatics applications.

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Fig. 1

Data availability

Prompts and scripts to support the conclusions are in Supplementary Files of the manuscript.

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Acknowledgements

NIH-NIGMS grants P20 GM103434, U54 GM-104942, and 1P20 GM121322 (GH). NIH-NIGMS Grant R01HG010805 and P20GM135008 to XG. NIH-NLM Grant No. R01LM013438 to LL. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The writing was polished by ChatGPT.

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Authors and Affiliations

  1. Department of Microbiology, Immunology & Cell Biology, West Virginia University, Morgantown, WV, 26506, USA

    Lei Wang & Gangqing Hu

  2. Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, 57007, USA

    Xijin Ge

  3. College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA

    Li Liu

  4. Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA

    Li Liu

Authors
  1. Lei Wang
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  2. Xijin Ge
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  3. Li Liu
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  4. Gangqing Hu
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Contributions

GH contributed to conceptualization, formal analysis, and writing—original draft; LW contributed to formal analysis; and XG and LL contributed to formal analysis, writing—review and editing.

Corresponding author

Correspondence to Gangqing Hu.

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Competing interests

The authors declared no competing interests.

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Associate Editor Stefan M. Duma oversaw the review of this article.

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Supplementary Information

Below is the link to the electronic supplementary material.

10439_2023_3324_MOESM1_ESM.pdf

Supplementary file1 (PDF 22130 kb). Supplementary File 1: Screen shot of chat session for requesting several gene expression data analysis. Supplementary File 2: Screen shot of chat session for requesting multiple gene sequence alignment. Supplementary File 3: Screen shot of chat session for requesting gene ID conversion. Supplementary File 4: Screen shot of chat session for requesting alignment of short sequencing reads. Supplementary File 5: Screen shot of chat session for requesting DE gene analysis based on a count matrix. Supplementary File 6: Screen shot of chat session for requesting phylogeny inference. Supplementary File 7: Screen shot of chat session for requesting a list of pre-installed Python packages

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Wang, L., Ge, X., Liu, L. et al. Code Interpreter for Bioinformatics: Are We There Yet?. Ann Biomed Eng 52, 754–756 (2024). https://doi.org/10.1007/s10439-023-03324-9

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  • DOI: https://doi.org/10.1007/s10439-023-03324-9

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