Checklist: Systems Biology Project Write-Up

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Below is a checklist adapted from a biostatistics lab report format for a semester-long Systems Biology project in which students designed their own biological/ecological system study and performed network analysis using R and Cytoscape.

(Network Analysis using R and Cytoscape)

In addition to this guideline, see:

 

Guidelines for reporting scientific research exist for many fields. These professional reporting standards can be highly technical. Our course goal is to communicate systems biology research clearly and transparently, using a lab-report style framework appropriate for student research projects.

Students in this course designed and investigated a biological or ecological system of their own choosing, using network analysis implemented in R and visualized in Cytoscape.

In addition to the written report, students must produce and share with the instructor a short video abstract summarizing their work. This mirrors the type of communication used by graduate students and researchers and can be included in a professional portfolio for internships, jobs, or graduate school applications.

The project report should be written in clear paragraphs rather than bullet lists, though sub-headings are encouraged to organize the report.

1. Introduction

State the research question clearly

  • What biological or ecological system are you studying?
  • What specific question about that system are you investigating?

Explain why the topic matters

  • Why is this system biologically, medically, or ecologically important?
  • What broader problem or concept does your work connect to?

Introduce the systems biology perspective

  • Briefly explain why network analysis or systems thinking is useful for studying this system.
  • Describe what types of interactions or relationships the network represents (e.g., species interactions, gene regulation, protein interactions, metabolic pathways, social interactions in ecology).

State the goal of the project

Example elements:

  • Constructing a network model
  • Analyzing network structure
  • Identifying key nodes or interactions
  • Exploring system-level properties

2. Methods

System Definition and Data Sources

Describe the biological or ecological system you modeled.

Include:

  • What entities are represented as nodes
  • What relationships are represented as edges
  • Where the data came from (literature, databases, simulated data, or observational data)

Examples:

  • Species interactions in an ecosystem
  • Gene regulatory network
  • Protein-protein interaction network
  • Disease transmission network
  • Food web

Network Construction

Explain how the network was built.

Include:

  • Node definition
  • Edge definition (directed, undirected, weighted, etc.)
  • Data preprocessing or cleaning
  • File format used for import (CSV, edge list, adjacency matrix)

Mention:

  • How the data were prepared for R
  • How the network was imported into Cytoscape

Computational Analysis (R)

Describe the network analysis performed in R.

Include:

  • Software packages used (for example: igraph, tidygraph, ggraph)
  • Network statistics calculated, such as:

Examples may include:

  • Degree distribution
  • Centrality measures
  • Clustering coefficient
  • Path length
  • Connected components
  • Network density
  • Modularity or community structure

Briefly explain why these metrics are useful for your research question.

Network Visualization (Cytoscape)

Describe how the network was visualized.

Include:

  • Layout used (force-directed, circular, hierarchical, etc.)
  • Visual encodings used, such as:
    • node color
    • node size
    • edge thickness
    • edge direction
  • What node or edge attributes were mapped to visual features.

Explain how the visualization helps interpret the system.

3. Results

Network Overview

Provide basic descriptive information about the network.

Examples:

  • Number of nodes
  • Number of edges
  • Directed or undirected network
  • Density or connectivity

Include a figure of the network visualization from Cytoscape.

Briefly describe the overall structure.

Network Analysis Findings

Report the key results from the R analysis.

Examples may include:

  • Nodes with highest degree or centrality
  • Identification of hubs
  • Presence of clusters or modules
  • Important pathways or interaction chains
  • Isolated components

Include relevant tables or plots if appropriate.

Key System Insights

Brief narrative describing what patterns were discovered.

Examples:

  • Which components appear most influential?
  • Are there clusters representing functional groups?
  • Does the structure suggest robustness, vulnerability, or hierarchy?

4. Discussion

Interpretation

Explain what your findings suggest about the biological system.

Possible discussion topics:

  • Role of highly connected nodes
  • Importance of specific interactions
  • Implications for ecosystem stability, disease spread, or molecular regulation
  • How network structure relates to system function

Strengths of the Approach

Explain why network analysis was useful.

Examples:

  • Revealed hidden relationships
  • Identified key system components
  • Provided a systems-level perspective

Limitations

Discuss limitations such as:

  • Small network size
  • Simplified or incomplete data
  • Assumptions in network construction
  • Lack of dynamic modeling
  • Potential missing interactions

Future Directions

What could improve or extend the analysis?

Examples:

  • Larger datasets
  • Time-series data
  • Dynamic or simulation models
  • Integration with additional biological data

5. Conclusion

Provide a brief 1–3 sentence summary answering your research question.

Your conclusion should state:

  • What you discovered about the system
  • Why it matters

6. Video Abstract

Students must produce a short video abstract summarizing their project.

The video should include:

  • The research question
  • The biological system studied
  • How the network was constructed
  • Key findings from the analysis
  • A visualization of the network
  • A brief conclusion

Length recommendation: 2–3 minutes.

Final Checks Before Turning In

✔ Research question clearly stated
✔ Biological or ecological system clearly defined
✔ Nodes and edges described clearly
✔ Data source or method of network construction explained
✔ R network analysis methods described
✔ Network statistics reported correctly
✔ Cytoscape visualization included and labeled
✔ Results interpreted clearly
✔ Discussion addresses strengths and limitations
✔ Conclusion answers the research question
✔ Writing is clear, concise, and organized in paragraphs
✔ Video abstract completed and submitted