bioepic-data

Sanity-check EcoSIM plant_trait.*.desc parameter values for the first grid only. Use when validating plant trait description files, reviewing one-plant-per-block trait records, or checking ranges, units, and woody/herbaceous block consistency before running EcoSIM.

Create EcoSIM Fortran namelist files and workable EcoSIM run folders for AmeriFlux site runs from site-specific grid, plant management, climate forcing, and greenhouse-gas inputs. Use when preparing or updating an EcoSIM `.namelist`, run folder, runfolder, run directory, or executable-ready site case for AmeriFlux or FLUXNET sites, especially after generating `*_ecosim_grid.nc`, `*_ecosim_climate.nc`, and `*_pft_mgmt.nc` inputs.

Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

Run the combined AmeriFlux to EcoSIM extraction workflow for site metadata, NADP or tDEP atmospheric chemistry, gSSURGO soil data, and optional climate or grid NetCDF forcing. Use when building a complete site-specific EcoSIM input package.

Download Copernicus CDS ERA5 single-level point time-series climate forcing for non-US or non-NLDAS EcoSIM sites from longitude/latitude coordinates. Use when a paper-derived site is outside the NLDAS domain, lacks AmeriFlux/FLUXNET curated forcing, or needs global ERA5 variables such as 2m temperature, dewpoint temperature, surface pressure, solar radiation, precipitation, and 10m wind components for EcoSIM preprocessing.

Estimate calcium-normalized Gapon selectivity coefficients for soil cation exchange from paired exchange-phase and solution-phase cation data. Use when deriving EcoSIM exchange parameters such as Ca-Na, Ca-Mg, Ca-K, Ca-NH4, Ca-Al, Ca-Fe, or Ca-H Gapon coefficients; when checking whether SSURGO, gSSURGO, WoSIS, SoilGrids, HWSD, lab, saturated-paste, groundwater, or soil-solution data can support Gapon calculations; or when converting exchangeable cation and liquid ion datasets into coefficient tables with unit, lyotropic-series, and mass-balance cautions.

Download, screen, and map non-North-America auxiliary EcoSIM climate variables from global or regional atmospheric-chemistry data sources. Use when a non-US/non-NLDAS site needs annual EcoSIM precipitation chemistry variables such as PHRG, CN4RIG, CNORIG, CSORG, CCARG, CMGRG, CNARG, CKARG, or CCLRG; when deciding whether to use CAMS, EBAS, EANET, or MERRA-2; or when deriving site-specific auxiliary variables after ERA5 climate forcing has been prepared.

Download NASA GES DISC NLDAS_FORA0125_H version 2.0 primary hourly forcing data for a point location. Use when Codex needs to retrieve NLDAS File A meteorological forcing from the GES DISC API or HTTPS archive for a longitude/latitude pair, including Earthdata username/password authentication, hourly URL generation, nearest-grid-point extraction, CSV output, or EcoSIM climate-forcing preprocessing.

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.

Query WFSFA watershed SFA soil moisture data in BERDL using generated schema references; use when answering questions about bervodata_watershed_sfa_soil_moisture tables, harmonized soil moisture observations, datasets, locations, ontology mappings, or composing BERDL queries that must adhere to the current table and column list.