Backend

Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Comprehensive software architecture skill for designing scalable, maintainable systems using ReactJS, NextJS, NodeJS, Express, React Native, Swift, Kotlin, Flutter, Postgres, GraphQL, Go, Python. Includes architecture diagram generation, system design patterns, tech stack decision frameworks, and dependency analysis. Use when designing system architecture, making technical decisions, creating architecture diagrams, evaluating trade-offs, or defining integration patterns.

Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

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.

Comprehensive backend development skill for building scalable backend systems using NodeJS, Express, Go, Python, Postgres, GraphQL, REST APIs. Includes API scaffolding, database optimization, security implementation, and performance tuning. Use when designing APIs, optimizing database queries, implementing business logic, handling authentication/authorization, or reviewing backend code.

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.

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

Add or modify WooCommerce backend PHP code following project conventions. Use when creating new classes, methods, hooks, or modifying existing backend code. **MUST be invoked before writing any PHP unit tests.**

This skill should be used when writing Ruby and Rails code in DHH's distinctive 37signals style. It applies when writing Ruby code, Rails applications, creating models, controllers, or any Ruby file. Triggers on Ruby/Rails code generation, refactoring requests, code review, or when the user mentions DHH, 37signals, Basecamp, HEY, or Campfire style. Embodies REST purity, fat models, thin controllers, Current attributes, Hotwire patterns, and the "clarity over cleverness" philosophy.

This skill should be used when writing Ruby and Rails code in DHH's distinctive 37signals style. It applies when writing Ruby code, Rails applications, creating models, controllers, or any Ruby file. Triggers on Ruby/Rails code generation, refactoring requests, code review, or when the user mentions DHH, 37signals, Basecamp, HEY, or Campfire style. Embodies REST purity, fat models, thin controllers, Current attributes, Hotwire patterns, and the "clarity over cleverness" philosophy.

This skill should be used when generating and editing images using the Gemini API (Nano Banana Pro). It applies when creating images from text prompts, editing existing images, applying style transfers, generating logos with text, creating stickers, product mockups, or any image generation/manipulation task. Supports text-to-image, image editing, multi-turn refinement, and composition from multiple reference images.

Human-readable control flow patterns for refactoring complex conditionals. Use when refactoring nested conditionals, improving code readability, or restructuring decision logic.

Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this skill when working with censored survival data, performing time-to-event analysis, fitting Cox models, Random Survival Forests, Gradient Boosting models, or Survival SVMs, evaluating survival predictions with concordance index or Brier score, handling competing risks, or implementing any survival analysis workflow with the scikit-survival library.

Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs, molecular property prediction, for geometric deep learning.

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.

Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.