ma-compbio-lab/skillfoundry
60 skills
$npx skills add ma-compbio-lab/skillfoundrySkillInstalls
admet-modeling-starterUse this starter when a task lands in the `ADMET modeling` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.agronomic-experiment-design-starterUse this starter when a task lands in the `Agronomic experiment design` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.ase-geometry-optimization-starterUse this skill to optimize a tiny argon dimer with ASE and summarize the final geometry.benchmarks-and-evaluation-starterUse this starter when a task lands in the `Benchmarks and evaluation` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.biosamples-sample-searchUse this skill to search EBI BioSamples for public sample metadata by text query or lightweight filters and return compact summaries.chembl-molecule-searchUse this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export.climate-ecology-integration-starterUse this starter when a task lands in the `Climate-ecology integration` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.climate-reanalysis-access-starterUse this starter when a task lands in the `Climate reanalysis access` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.clinicaltrials-study-searchUse this skill to search the current ClinicalTrials.gov v2 API for condition or keyword matches when you need official clinical-study metadata. Do not use it for legacy API URLs or offline work.conservation-genomics-and-edna-starterUse this starter when a task lands in the `Conservation genomics and eDNA` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.crop-genomics-and-breeding-starterUse this starter when a task lands in the `Crop genomics and breeding` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.deepchem-circular-featurizationUse this skill to compute compact DeepChem circular fingerprints from a small set of SMILES strings with the repo-managed DeepChem prefix. Do not use it for model training, docking, or large library sdeepchem-molgraph-featurizationUse this skill to featurize SMILES strings into DeepChem molecular graph objects. Prefer it for local graph-based preprocessing before molecular machine-learning experiments.disease-and-stress-detection-starterUse this starter when a task lands in the `Disease and stress detection` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.ecosystem-remote-sensing-starterUse this starter when a task lands in the `Ecosystem remote sensing` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.ehr-preprocessing-starterUse this starter when a task lands in the `EHR preprocessing` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.fairlearn-bias-audit-starterUse this skill to run a deterministic group fairness audit over a tiny clinical toy cohort with `fairlearn`.food-chemistry-and-quality-modeling-starterUse this starter when a task lands in the `Food chemistry and quality modeling` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.free-energy-workflows-starterUse this starter when a task lands in the `Free-energy workflows` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.frictionless-tabular-validation-starterUse this skill to validate a small CSV or TSV table against a simple Frictionless schema and emit a compact machine-readable error summary.gbif-dataset-search-starterUse this skill to query the official GBIF dataset-search API and summarize a small biodiversity dataset result set.gbif-species-occurrence-search-starterUse this skill to query the official GBIF API for a canonical species match and a small live occurrence sample.geopandas-spatial-join-starterUse this skill to run a deterministic point-in-polygon join with GeoPandas and summarize the result in compact JSON.lifelines-kaplan-meier-starterUse this skill to run a deterministic Kaplan-Meier survival analysis over a toy cohort and summarize per-group survival curves.metadata-harmonization-starterUse this skill to harmonize small metadata tables with inconsistent column names and categorical labels into one canonical TSV plus a compact JSON summary.missing-data-handling-starterUse this starter when a task lands in the `Missing-data handling` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.molecular-generation-starterUse this starter when a task lands in the `Molecular generation` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.numcodecs-compression-decompression-starterUse this skill to round-trip a small integer matrix through a deterministic `numcodecs` compressor and inspect the encoded payload summary.openmm-forcefield-assignment-starterUse this skill to assign a simple water force field to a tiny PDB topology with OpenMM and summarize the resulting system.openmm-langevin-dynamics-starterUse this skill to run a deterministic toy Langevin dynamics simulation in OpenMM and inspect a compact trajectory summary.openmm-system-minimizationUse this skill to run a deterministic OpenMM energy minimization on a tiny toy system. Do not use it for production molecular dynamics or force-field validation.phenotyping-starterUse this starter when a task lands in the `Phenotyping` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.physics-informed-forecasting-starterUse this starter when a task lands in the `Physics-informed forecasting` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.plantcv-plant-phenotyping-starterUse this skill to generate a tiny synthetic plant image, segment it with `PlantCV`, and summarize simple morphology-style phenotyping measurements.population-dynamics-and-ecological-forecasting-starterUse this starter when a task lands in the `Population dynamics and ecological forecasting` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.precision-agriculture-sensing-starterUse this starter when a task lands in the `Precision agriculture sensing` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.privacy-preserving-analysis-starterUse this starter when a task lands in the `Privacy-preserving analysis` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.psi4-single-point-energyUse this skill to run a deterministic Psi4 single-point Hartree-Fock energy on a tiny water molecule. Do not use it for production quantum chemistry benchmarking or large basis-set studies.pyarrow-format-conversion-starterUse this skill to convert a small tabular file into Parquet with PyArrow and inspect a deterministic round-trip summary.qm-mm-workflows-starterUse this starter when a task lands in the `QM/MM workflows` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.qsar-property-prediction-starterUse this starter when a task lands in the `QSAR / property prediction` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.quantum-chemistry-setup-starterUse this starter when a task lands in the `Quantum chemistry setup` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.raster-vector-ingestion-starterUse this starter when a task lands in the `Raster / vector ingestion` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.rasterio-windowed-raster-preprocessing-starterUse this skill to generate a tiny toy raster with Rasterio, extract a window, downsample it, and summarize the preprocessing result in compact JSON.rdkit-conformer-generation-starterUse this skill to generate a small deterministic conformer ensemble with RDKit ETKDG and summarize the lowest-energy structures.rdkit-molecular-descriptorsUse this skill to compute compact cheminformatics descriptors from one SMILES string with RDKit. Do not use it for docking, quantum chemistry, or large library screening.rdkit-molecule-standardizationUse this skill to standardize one small-molecule SMILES string with RDKit MolStandardize. It is for local cleanup, salt stripping, uncharging, and tautomer canonicalization, not docking or batch-librardkit-scaffold-analysis-starterUse this skill to compute Murcko scaffold summaries for a small local molecule set with RDKit. Prefer it for deterministic scaffold grouping and smoke-scale cheminformatics checks.rocrate-metadata-bundle-starterUse this skill to package a small local data file into an RO-Crate directory with basic provenance-rich metadata and a compact summary of the generated graph.scientific-map-and-dashboard-generation-starterUse this starter when a task lands in the `Scientific map and dashboard generation` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.scikitbio-tree-comparison-starterUse this skill to parse two small Newick trees with `scikit-bio` and summarize a compact topology-comparison result.soil-rhizosphere-microbiome-analysis-starterUse this starter when a task lands in the `Soil / rhizosphere / microbiome analysis` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.spatial-interpolation-and-uncertainty-starterUse this starter when a task lands in the `Spatial interpolation and uncertainty` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.synthetic-toy-dataset-generator-starterUse this skill to generate a deterministic tiny dataset bundle for tests, demos, and smoke fixtures.time-series-clinical-modeling-starterUse this starter when a task lands in the `Time-series clinical modeling` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.trajectory-analysis-starterUse this starter when a task lands in the `Trajectory analysis` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.virtual-screening-starterUse this starter when a task lands in the `Virtual screening` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.xarray-climate-cube-starterUse this skill to build a deterministic toy climate cube with Xarray and summarize simple spatiotemporal statistics.yield-forecasting-starterUse this starter when a task lands in the `Yield forecasting` frontier leaf and the repository has curated resources but no dedicated runtime implementation yet.zarr-chunked-array-store-starterUse this skill to convert a small numeric matrix into a chunked, compressed Zarr store and inspect a deterministic summary of its layout.