SkillFoundry

Use 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.

Use this skill to resolve a gene symbol to Ensembl IDs and fetch a canonical Ensembl gene record. Do not use it for full transcript annotation pipelines or offline work.

Use this skill to search NCBI Gene by symbol and organism, then fetch compact official Entrez Gene summaries. Do not use it for variant interpretation, transcript-level modeling, or bulk offline annotation.

Use this skill to author and run a minimal Common Workflow Language CommandLineTool and one-step workflow with cwltool. Do not use it for containerized production execution or complex scatter/gather workflows.

Use this skill to run a minimal Nextflow workflow through the repo-managed Java and Nextflow prefix, either locally or on the Slurm cluster. Do not use it for containerized production pipelines.

Use this skill to verify the repo-managed nf-core tools install and retrieve a cleaned summary of available pipelines. Do not use it for interactive launch flows or full pipeline downloads.

Use this skill to run a tiny Snakemake workflow through the repo-managed Snakemake prefix and inspect deterministic toy outputs.

Use this skill to author and run a minimal WDL task and workflow with miniwdl. Do not use it for Cromwell-specific backends or large imported workflow graphs.

Use this skill to featurize SMILES strings into DeepChem molecular graph objects. Prefer it for local graph-based preprocessing before molecular machine-learning experiments.

Use 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.

Use 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.

Use this skill to search EBI BioSamples for public sample metadata by text query or lightweight filters and return compact summaries.

Use 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.

Use 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 screening.

Use 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.

Use 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-library processing.

Use 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.

Use this skill to search ENCODE experiments by assay or free-text keyword and return compact metadata summaries for public epigenomics records.

Use this skill to render, submit, and inspect a minimal Slurm smoke job before submitting heavier workloads on a real cluster.

Use this skill to search MetaboLights studies and resolve a compact summary for each matched accession through the official JSON API.

Use this skill to fetch a compact accession summary from the EBI Proteins API. Do not use it for bulk downloads, unsupported endpoints, or full protein annotation export.

Use this skill to search PRIDE Archive v2 proteomics projects by keyword and return compact dataset-discovery summaries. Do not use it for raw file download orchestration or unsupported PRIDE endpoints.

Parse small benchmark markdown tables from paper notes and summarize datasets, metrics, and best-performing methods.

Use this skill to search Crossref metadata when you need DOI-oriented citation records from the official REST API. Do not use it when you need full text or publisher-specific access controls.

Extract likely dataset, code, and package links from locally prepared paper text or markdown using deterministic URL and keyword rules.

Use this skill to search life-science literature through Europe PMC when you need publication metadata oriented toward biomedical method triage. Do not use it when you need offline execution or cluster-scale batch processing.

Extract figure and table captions from locally prepared paper text using deterministic caption patterns.

Use this skill to query OpenAlex, Europe PMC, Crossref, and PubMed for the same topic and build a normalized literature brief. Do not use it as a full systematic-review workflow or citation-analysis engine.

Use this skill to search PubMed through NCBI E-utilities when you need official Entrez-backed literature discovery and summary metadata. Do not use it when you need full text or network-free execution.

Use this skill to run fast literature triage against OpenAlex when you need public paper metadata, citation-linked context, and structured JSON output. Do not use it when you need full text, proprietary databases, or offline execution.

Rank a small set of candidate papers for triage using deterministic citation, recency, and query-overlap heuristics inspired by Semantic Scholar recommendation workflows.

Mine likely review, survey, and meta-analysis papers from a local metadata set using deterministic title and abstract heuristics aligned with Semantic Scholar review-search workflows.

Use this skill to fetch a canonical RCSB PDB entry record by accession when you need quick structural metadata. Do not use it for search ranking or full structure parsing pipelines.

Use this skill to search the Protein Data Bank through the official RCSB Search API when you need structure identifiers from a free-text query. Do not use it when you need structure download or coordinate parsing.

Use this skill to run deterministic local custom enrichment with Bioconductor clusterProfiler and user-supplied TERM2GENE tables. Do not use it for remote annotation downloads or organism database lookups.

Use this skill to run deterministic toy or local custom preranked gene-set enrichment with Bioconductor fgsea. Do not use it for remote annotation lookups or large cohort-scale pathway workflows.

Use this skill to fetch a concise summary for a known Reactome event or pathway stable ID from the official Reactome Content Service. Do not use it for full pathway traversal, graph expansion, or unsupported Reactome endpoints.

Use this skill to submit a short identifier list to Reactome Analysis Service and return compact pathway enrichment summaries. Do not use it for full downstream statistical analysis or unsupported identifier normalization.

Use this skill to run a lightweight Scanpy QC pass on a toy count matrix with the repository-managed Scanpy environment.