15.2 Project: GenAI for Graphical Abstracts

15.2.1 Purpose

In this project, you will create the first panel of a Graphical Abstract (GA) for your research project work. This GA building activity is meant to parallel your research project progress and to reflect your evolving ideas around the key question you want to address in your research, datasets you will use to answer your questions, and methods you will employ to do so.

See Xue et al. 2023 Ballast Water Case Study example

15.2.2 Learning Objectives

  1. Create the first panel (Context) for a graphical abstract (Context/Methods/Findings)
  2. Practice planning and critically evaluating GenAI

15.2.3 Introduction

One framework for graphical abstracts is comprised of three panels

  • Context – Introduce your question, datasets, samples, metadata
  • Method – Snapshot of the Galaxy workflow you used to analyze data
  • Findings - Summarize your main conclusion

Once you get to the end of the course, you will have all pieces together to put together a GA, and should use all tools available to you to do so - GenAI, manual figures, snapshots, etc. For the next five weeks of your project work phase, you will focus on using GenAI for only the first panel to convey the Context by integrating questions, datasets, samples, and metadata.

A second goal is to practice prompt engineering - a fundamental AI literacy skill - to help develop stronger scientific communication skills. Prompting is a natural language skill and involves creating clear, contextual instructions (prompts) to guide AI models to perform tasks effectively. By iteratively using GenAI to develop your GA, you have the opportunity to hone your scientific communication skills through improved prompts as you gain subject matter expertise (you are doing the research, you are the expert!)

15.2.4 Activity 1 - Plan your prompt

Estimated time: 5 min

15.2.4.1 Instructions

  1. Describe the topic you have proposed for your capstone project.
    1. Pick a research theme you want to explore (e.g. antibiotic resistance, pathogen detection, microbial diversity, microbes and disease, microbes of a specific environment, etc)
  2. Describe the long-read datasets that you have identified for your topic.
    1. Identify a publicly available dataset you can analyze for your question. Aim for a dataset with clear metadata and a linked publication when possible.
  3. Structure your prompts around the pillars of prompting which include:
    1. Task - a sentence that starts with an action (e.g. create, remake from scratch, modify, adjust, clarify, etc.)
      • “Create a graphical abstract”
    2. Format - structure of output (e.g. style of image)
      • “Create a graphical abstract … with a simple style”
    3. Context - topic of interest, background info (e.g. datasets, sample metadata)

Note: It is fine to change your mind later and pursue a different dataset and/or a different topic; If you change your mind later, you can revise your approach in later GenAI project iterations

15.2.4.2 Questions

1. Write a draft research question. In 1-2 sentences, describe what you want to find out and why the dataset is a good fit.

  1. Identify key prompt 1 features.
Prompt Feature Your info (bullet points)
Task
Format
Context (Details)

15.2.5 Activity 2 - Prepare Graphical Abstract

Estimated time: 15 min

15.2.5.1 Instructions

  1. Using prompt text, generate GA using GenAI tool of your choice
  2. Do as many attempts as can do in 15 min, logging each attempt’s prompt/output/evaluation

15.2.5.2 Questions

Prompt #1, Graphical Abstract #1

1. Enter prompt text

2. Paste the resulting GA image below

  1. Evaluate GA output
Evaluation Your Answer
Provide overall description/critique of the GA output
Name 2 specific things you would modify in the output GA

Prompt #2, Graphical Abstract #2

1. Enter modified prompt text

2. Paste the resulting GA image below

  1. Evaluate GA output
Evaluation Your Answer
Provide overall description/critique of the GA output
Name 2 specific things you would modify in the output GA

Prompt #3, Graphical Abstract #3

1. Enter modified prompt text

2. Paste the resulting GA image below

  1. Evaluate GA output
Evaluation Your Answer
Provide overall description/critique of the GA output
Name 2 specific things you would modify in the output GA

Prompt #4, Graphical Abstract #4

1. Enter modified prompt text

2. Paste the resulting GA image below

  1. Evaluate GA output
Evaluation Your Answer
Provide overall description/critique of the GA output
Name 2 specific things you would modify in the output GA

15.2.6 Activity 3 - Reflect on your GenAI experience

Estimated time: 5 min

15.2.6.1 Instructions

  1. Discuss your experience and outcomes in this Activity by answering questions below.

15.2.6.2 Questions

1. What aspects of the graphical abstract were done well by GenAI? Where did GenAI do poorly?

2. Was GenAI a helpful assistant for this activity?

3. Do you have concerns about using GenAI for this assignment?

15.2.7 Grading Criteria

  • Download as Microsoft Word (.docx) and upload on Canvas

15.2.8 Footnotes

Resources

Contributions and Affiliations

  • Valeriya Gaysinskaya, Johns Hopkins University
  • Frederick Tan, Johns Hopkins University

Last Revised: February 2026

All materials CC-BY unless noted otherwise.