synthesize

name	synthesize
description	Read analysis outputs, compare against literature, and draft findings for EcoSIM-focused reports in this repository.
allowed-tools	Bash, Read, Write, Edit, WebSearch, AskUserQuestion
user-invocable	true

Synthesis Skill

Synthesize analysis outputs into a report that connects numerical results, literature context, and implications for EcoSIM calibration and validation.

Compatibility Modes

• Full mode: local analysis outputs plus MCP literature review.
• Limited mode: synthesize from local outputs only and flag literature gaps explicitly.

Usage

/synthesize [topic-or-folder]

If no argument is provided, infer scope from the current directory and recent modified analysis artifacts.

Workflow

Step 1: Gather Context

Collect:

• Analysis outputs under derived/, output/, netcdf/, and relevant notebooks
• Study summaries (derived/*/summary.md)
• Metadata (derived/*/metadata.yaml)
• Existing benchmark tables in hackathon-case_study-experimental_warming_nitrogen/derived/

Step 2: Extract Results

From CSV/TSV/notebook outputs, summarize:

• Main effect sizes and uncertainty
• Directional results by ecosystem/site
• Statistical significance or confidence ranges
• Any anomalies or missingness patterns

Step 3: Validate Interpretation with User

Present a draft interpretation and ask for corrections before finalizing report text.

Step 4: Literature Cross-Reference

Call literature-review for supporting/contradictory evidence and methodological context.

Step 5: Draft Report

Write or update a report at one of:

• docs/reports/<topic>.md (preferred)
• output/reports/<topic>.md
• derived/<study-id>/summary.md (when extending an existing packet)

Suggested structure:

# Report: <title>

## Key Findings
- <finding with numbers>

## Results
- <tables/figures and interpretation>

## Literature Context
- <agreement, disagreement, novelty>

## Limitations
- <coverage, assumptions, confounders>

## Relevance to EcoSIM
- <parameterization, forcing, validation implications>

## Next Steps
1. <next analysis>
2. <data needed>
3. <model experiment>

## References
- <citations>

Step 6: Update Pointers

If creating a new report, add a short link/reference in README.md or the relevant derived/*/summary.md.

Integration

• Reads: repo-local analysis artifacts and metadata
• Calls: literature-review
• Produces: report markdown for decision-making and follow-on modeling

Pitfall Handling

Document major surprises, constraints, and assumptions explicitly in the report. Prefer transparent caveats over silent omission.