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Benchling Integration Toolkit

benchling-integration

K-Dense-AI/claude-scientific-skills

Automate Benchling lab data workflows via the Python SDK or REST API: manage registry entities (DNA, proteins), inventory, ELN entries, workflows, and Data Warehouse queries for syncing and analytics.

ClinPGx Database Access

clinpgx-database

K-Dense-AI/claude-scientific-skills

Provide REST API access to ClinPGx, the successor to PharmGKB, for querying gene-drug interactions, CPIC/DPWG/FDA guidelines, allele functions, and evidence that supports precision dosing and pharmacogenomics-driven clinical decisions.

ENA Sequence Access

K-Dense-AI/claude-scientific-skills

Access the European Nucleotide Archive via REST/FTP to fetch DNA/RNA sequences, raw reads, assemblies, annotations, and taxonomy for research or bioinformatics pipelines.

Ensembl Genome API

ensembl-database

K-Dense-AI/claude-scientific-skills

Query Ensembl’s RESTful API to access gene annotations, sequences, variants, orthologs, and assembly mappings across 250+ species, enabling integration into genomic research pipelines.

FRED Economic Data API

fred-economic-data

K-Dense-AI/claude-scientific-skills

Access over 800,000 economic time series from FRED's API, covering GDP, employment, inflation, interest rates, regional metrics, and more; ideal for macroeconomic analysis, financial research, policymaking, and forecasting workflows.

GWAS Catalog Access

K-Dense-AI/claude-scientific-skills

Query the NHGRI-EBI GWAS Catalog for SNP-trait associations, fetch study metadata, variant and trait details, and download summary statistics via the web or REST APIs to support genetic epidemiology and polygenic risk modeling.

KEGG REST Toolkit

K-Dense-AI/claude-scientific-skills

Direct Python helpers for KEGG's REST API, covering database metadata, listing, search, retrieval, ID conversion, linkage, and drug interactions to power pathway and gene analysis.

Metabolomics Workbench API

metabolomics-workbench-database

K-Dense-AI/claude-scientific-skills

Query the NIH Metabolomics Workbench via REST API to fetch metabolites, RefMet nomenclature, mass-spec searches, and detailed study datasets for biomarker discovery and metabolomics research.

Open Notebook Research Hub

K-Dense-AI/claude-scientific-skills

Self-hosted open-source alternative to NotebookLM for organizing research, ingesting diverse sources, generating AI notes, running context-aware chats, performing vector search, producing multi-speaker podcasts, and automating workflows via a REST API.

PubChem Database Query

pubchem-database

K-Dense-AI/claude-scientific-skills

Leverages PubChem’s PUG-REST API or PubChemPy to search 110M+ compounds by name, CID, or structure, fetch properties, perform similarity/substructure lookups, and access bioactivity or format conversions for cheminformatics workflows.

PubMed Database Access

pubmed-database

K-Dense-AI/claude-scientific-skills

Direct REST/API access to PubMed for constructing complex Boolean or MeSH queries, filtering by publication attributes, and automating literature retrieval or citation management via NCBI’s E-utilities.

Seatbelt Sandbox Generator

seatbelt-sandboxer

trailofbits/skills

Generates minimal macOS Seatbelt sandbox profiles with allowlist-based resource rules so apps can be isolated by permissions, useful for restricting file, network, and IPC access when defending against high-risk execution or supply chain threats.

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