SCRIPT LINE
APIs discovered by reading code, migrations held together by hope.
Contracts written first, migrations rehearsed before they run.
110 skills on this line
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
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.
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
Creates and validates 7 project docs (requirements, architecture, tech_stack, api_spec, database_schema, design_guidelines, runbook). Fourth worker in ln-110-documents-pipeline.
Creates test documentation (testing-strategy.md + tests/README.md). Establishes testing philosophy and Story-Level Test Task Pattern. Part of ln-110-documents-pipeline workflow.
CREATE/REPLAN Epics from scope (3-7 Epics). Batch Preview + Auto-extraction. Decompose-First Pattern. Auto-discovers team ID.
CREATE/REPLAN Stories for Epic (5-10 Stories). Delegates ln-221-standards-researcher for standards research. Decompose-First Pattern. Auto-discovers team/Epic.
Research standards/patterns via MCP Ref. Generates Standards Research for Story Technical Notes subsection. Reusable worker.
Convert markdown documents and chat summaries into formatted EPUB ebook files that can be read on any device or uploaded to Kindle.
Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.
Deterministic mathematical computation using SymPy. Use for ANY math operation requiring exact/verified results - basic arithmetic, algebra (simplify, expand, factor, solve equations), calculus (derivatives, integrals, limits, series), linear algebra (matrices, determinants, eigenvalues), trigonometry, number theory (primes, GCD/LCM, factorization), and statistics. Ensures mathematical accuracy by using symbolic computation rather than LLM estimation.
Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
Generate highly detailed, Midjourney-style image prompts optimized for the FLUX 1.1 Pro model on Replicate. Transform basic user descriptions into rich, cinematic prompts with professional photography qualities, dramatic lighting, and editorial-quality aesthetics. Use when users request image generation, need prompt enhancement, or want Midjourney-quality outputs via FLUX 1.1 Pro.
Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.