القائمة
Review repository evidence and propose high-impact next research directions for EcoSIM, emphasizing warming-nitrogen mechanisms, data readiness, and methodological feasibility.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
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.
Read analysis outputs, compare against literature, and draft findings for EcoSIM-focused reports in this repository.
| name | suggest-research |
| description | Review repository evidence and propose high-impact next research directions for EcoSIM, emphasizing warming-nitrogen mechanisms, data readiness, and methodological feasibility. |
| allowed-tools | Bash, Read, Write, Edit, WebSearch, AskUserQuestion |
| user-invocable | true |
Identify and prioritize the next research topic using available EcoSIM-relevant data and completed analyses in this repository.
/suggest-research
Read and summarize key inputs:
derived/*.tsv datasetsderived/*/summary.md and derived/*/metadata.yamlbervo/bervo-terms.tsvhackathon-case_study-experimental_warming_nitrogen/derived/*.tsvPLANT_TRAITS.md and hackathon-case_study-experimental_warming_nitrogen/plant_traits.jsonFrom summaries and metadata, capture:
For each candidate topic, check:
If the user has not specified preferences, ask:
Use this rubric:
| Criterion | Weight |
|---|---|
| Scientific novelty | High |
| Data readiness | High |
| Potential impact | High |
| Feasibility | Medium |
| Reuse of existing assets | Medium |
| Effort fit | Low |
Pick one primary recommendation plus one alternative.
Run literature-review for the top candidate to confirm:
Provide:
If user approves, append to docs/research_ideas.md (create if missing) with status PROPOSED.
Do not require BERIL-specific project scaffolding commands.
literature-review for novelty checksdocs/research_ideas.mdIf blocked by missing inputs or contradictory metadata, record concise notes in repo memory and surface assumptions in the recommendation.