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Read analysis outputs, compare against literature, and draft findings for EcoSIM-focused reports in this repository.
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
Retrieve and use BERDL MinIO credentials and transfer result artifacts between BERDL object storage and the local machine. Use when exported query results need to be listed, downloaded, shared, or when only KBASE_AUTH_TOKEN is available and MinIO keys must be acquired.
Run SQL queries from a local machine against a provisioned BERDL Spark cluster using spark_connect_remote. Use when the user wants remote Spark compute with local control, needs clarity on connection and timeout behavior, or wants to return small/medium results directly before exporting large outputs.
Discover and document BERDL databases. Use when the user wants to explore a new database, generate documentation for a database, or create a module file for the berdl skill.
Query the KBase BERDL (BER Data Lakehouse) databases. Use when the user asks to explore pangenome data, query species information, get genome statistics, analyze gene clusters, access functional annotations, or query biochemistry data.
Search and review ecosystem and biogeochemical literature using MCP tools (PubMed, arXiv, bioRxiv, Google Scholar), with optional full-text reading and citation snowballing. Use when the user needs evidence, citations, methods comparison, or novelty checks for EcoSIM and warming-nitrogen hypotheses.
Review repository evidence and propose high-impact next research directions for EcoSIM, emphasizing warming-nitrogen mechanisms, data readiness, and methodological feasibility.
| 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 |
Synthesize analysis outputs into a report that connects numerical results, literature context, and implications for EcoSIM calibration and validation.
/synthesize [topic-or-folder]
If no argument is provided, infer scope from the current directory and recent modified analysis artifacts.
Collect:
derived/, output/, netcdf/, and relevant notebooksderived/*/summary.md)derived/*/metadata.yaml)hackathon-case_study-experimental_warming_nitrogen/derived/From CSV/TSV/notebook outputs, summarize:
Present a draft interpretation and ask for corrections before finalizing report text.
Call literature-review for supporting/contradictory evidence and methodological context.
Write or update a report at one of:
docs/reports/<topic>.md (preferred)output/reports/<topic>.mdderived/<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>
If creating a new report, add a short link/reference in README.md or the relevant derived/*/summary.md.
literature-reviewDocument major surprises, constraints, and assumptions explicitly in the report. Prefer transparent caveats over silent omission.