ORM

Optimize AgentDB performance with quantization (4-32x memory reduction), HNSW indexing (150x faster search), caching, and batch operations. Use when optimizing memory usage, improving search speed, or scaling to millions of vectors.

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies.

Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and actionable feedback.

Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.

Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis.

Profile code performance using callgrind and valgrind with nextest integration for analyzing instruction counts, cache behavior, and identifying bottlenecks

Query and analyze SEC filings and financial statements using EdgarTools. Get company data, filings, XBRL financials, and perform multi-company analysis.

Use when receiving code review feedback (especially if unclear or technically questionable), when completing tasks or major features requiring review before proceeding, or before making any completion/success claims. Covers three practices - receiving feedback with technical rigor over performative agreement, requesting reviews via code-reviewer subagent, and verification gates requiring evidence before any status claims. Essential for subagent-driven development, pull requests, and preventing false completion claims.

Deploy and manage cloud infrastructure on Cloudflare (Workers, R2, D1, KV, Pages, Durable Objects, Browser Rendering), Docker containers, and Google Cloud Platform (Compute Engine, GKE, Cloud Run, App Engine, Cloud Storage). Use when deploying serverless functions to the edge, configuring edge computing solutions, managing Docker containers and images, setting up CI/CD pipelines, optimizing cloud infrastructure costs, implementing global caching strategies, working with cloud databases, or building cloud-native applications.

Use CloudBase HTTP API to access CloudBase platform features (database, authentication, cloud functions, cloud hosting, cloud storage, AI) via HTTP protocol from backends or scripts that are not using SDKs.

CloudBase platform knowledge and best practices. Use this skill for general CloudBase platform understanding, including storage, hosting, authentication, cloud functions, database permissions, and data models.

Use CloudBase Auth tool to configure and manage authentication providers for web applications - enable/disable login methods (SMS, Email, WeChat Open Platform, Google, Anonymous, Username/password, OAuth, SAML, CAS, Dingding, etc.) and configure provider settings via MCP tools.

Analyzes and optimizes application performance across frontend, backend, and database layers. Use when diagnosing slowness, improving load times, optimizing queries, reducing bundle size, or when asked about performance issues.