Institution:   University of Galway

Discipline:   Pharmacology

Authors:   Jack McGoldrick,  Ronan Fleming

GenAI tool(s) used: ChatGPT

Situation / Context

The project was undertaken by a final year undergraduate student, completing his research project in the discipline of Pharmacology. Only one student was involved in this project. The student was tasked with identifying common biophysical properties of a set of proteins found to be metabolically associated with Parkinson’s Disease. This task would involve the student utilising a computer programming language in the form of Python. The student had no prior exposure to computer programming.

Task / Goal

The project aimed to improve the computer programming skills of the student sufficiently, so that they could complete their project as described. The student had no prior knowledge of any computer programming languages, with their background being in Biology and Pharmacology. ChatGPT was used as a personal tutor to the student throughout the project. The student was encouraged to use ChatGPT for any questions or problems they encountered, including understanding of new syntax, querying for modules/ libraries which may be helpful, understanding error outputs etc. The student also queried ChatGPT for other resources which may have been helpful including books, tutorials, and websites. Programming advice was available to the student including guidance from more experienced PhD students within the project, and their supervisor. The student was hesitant at first, being exposed to a new skill, at a vital time in their undergraduate degree, but embraced the challenge and ultimately succeeded in completing his project.

Actions / Implementation

The student initially met with their supervisor to get set up and begin their project. The student was introduced to Python and was provided with a few examples of how to start their project. The student was then left to work in their own way, with weekly meetings to track progress.

The student used Jupyter notebook to complete their work. For example, he began by working with data frames which contained initial information on genes of relevance. The student used Python to convert from gene names to relevant proteins produced by the genes. He achieved this via a Python library called ‘pandas’. The student leveraged ChatGPT to explain what pandas were, what data types they handled and how data frames could be manipulated using it. The student gained valuable insights into a Python library and applied their new knowledge to their project.

This is just one example of how ChatGPT was leveraged in his project. He also leveraged ChatGPT to help understand coding standards that needed to be followed to ensure reproducibility of his experiments and proper file and data management practices. The student used ChatGPT as a resource to aid in all the new aspects he encountered in his project, which aided him in learning new skills vital to his education.

Outcomes

The primary outcome was the enhanced rate at which the student was able to learn a new programming language. The student used Python throughout their entire project via numerous routes including conversion of data frames, construction and analysis of protein-protein interaction networks, gene enrichment analysis and statistical analysis. All of this was achieved in a 3-month period, the length of his final year project.

The student became proficient in Python and has even become a member of the research group after completing his degree. ChatGPT played a vital role as a learning resource throughout his project and enhanced the rate at which he was able to learn. Clearly, ChatGPT has a significant use as a learning aid. No formal form of evaluation was carried out due to the nature of the project, but the student performed well throughout the project achieving a high grade.

Reflections

ChatGPT can be used as a learning resource to aid students in the process of computer programming. This project used Python as the language of choice, but this could be applied to any programming language.

It was not expected that ChatGPT would be so efficient in aiding the student’s learning, especially in such a brief time frame. Perhaps, next time a few examples of how to effectively utilise ChatGPT to aid in your learning could be provided to further aid students.

ChatGPT can be used as a learning aid in conjunction with other methods. The student enjoyed their project, particularly learning Python and how it can be used for scientific purposes. The student mentions that ChatGPT is a helpful resource and helped significantly but should not be heavily relied on as it may be counterproductive if queried for every matter. It should be used as an aid to learn, not a method of bypassing learning.

Author Biography

Jack McGoldrick was the student who completed this research project. He recently completed his undergraduate degree in Pharmacology and is now currently working as a research assistant within Recon4IMD at the University of Galway before starting his PhD.

Dr Ronan Fleming is a Senior Lecturer in the College of Medicine at the University of Galway and was the PI on this project. Dr Fleming leads the Systems Biochemistry Group in the University of Galway and is the coordinator of ‘Reconstruction and Computational Modelling for Inherited Metabolic Diseases (Recon4IMD), a Horizon Europe Research and Innovation action funded study.