Mental Model

This section captures your current working theory of the biological or computational system under study. It's where you articulate how you think the system works even if that model is provisional or incomplete.

Current Conceptual Model

• How do you currently believe the relevant biological process or system operates?
• What entities (e.g., genes, pathways, cell types, clinical features) and relationships are central to the model?
• What is the directional flow of influence (e.g., variant → gene expression → phenotype)?

Visual Diagram (if applicable)

• Sketch or link to a diagram representing your model.
• Include key components (inputs, intermediates, outputs) and their hypothesized interactions.
• Label assumptions or areas of uncertainty.

Assumptions Holding the Model Together

• Are relationships assumed to be linear, monotonic, or causal?
• Is stationarity, independence, or time-invariance assumed?
• Are proxies being used for latent or unmeasured variables?
• What known limitations or biological unknowns could disrupt this model?

Competing or Simpler Models

• Are there published models or frameworks that contrast with yours?
• Could a more parsimonious explanation (e.g., statistical artifact, batch effect) account for observed patterns?
• How would you test whether your model outperforms or is more explanatory than alternatives?