ecosim-co-scientist

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.

Read analysis outputs, compare against literature, and draft findings for EcoSIM-focused reports in this repository.

Capture non-obvious errors, data caveats, and performance gotchas discovered during analysis into repository memory for reuse.

Download ERA5 climate reanalysis data from the Copernicus Climate Data Store using cdsapi. Use this skill when users request ERA5 data, climate forcing data, meteorological variables, or need to download atmospheric/land surface data for ecosystem modeling, climate analysis, or model validation.

Extract and analyze metadata from NetCDF files. Use this skill when working with NetCDF (.nc) or CDL (.cdl) files to extract variable information, dimensions, attributes, and data types to CSV format for documentation and analysis.