Claude Skills by bg-szy

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use when validating RNA-seq libraries before differential expression analysis.

End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comp...

Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.

Bulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.

Operate long-lived agent workloads with observability, security boundaries, and lifecycle management.

Apple FoundationModels framework for on-device LLM — text generation, guided generation with @Generable, tool calling, and snapshot streaming in iOS 26+.

Install and operate Hermes Tweet, a Hermes Agent plugin for X/Twitter research, timeline reading, tweet analysis, and approval-gated private or state-changing operations. Use this skill when installing Hermes Tweet, researching X/Twitter accounts, monitoring launch signals, investigating mentions, auditing giveaways, or preparing gated X operations. Use proactively when a Hermes Agent workflow needs current X/Twitter context. Requires XQUIK_API_KEY for read and action tools.

Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align),...

Operate and extend NanoClaw v2, ECC's zero-dependency session-aware REPL built on claude -p.

Create, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outputs. Use for paper or scientific plots, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化. Define the conclusion, evidence logic, data integrity, template compatibility, export needs, and reviewer...

Polish, restructure, or translate academic prose into concise Nature-leaning English while preserving facts, evidence boundaries, terminology, and citation intent. Use for manuscript paragraphs, abstracts, introductions, Results, discussions, conclusions, titles, Methods, Chinese drafts, proofreading, language editing, and general academic or scientific writing. Also use to shorten bloated Results, allocate evidence across main text, captions, and Supplementary Information, prevent reviewer-d...

Internal shared-reference support package for installed Nature Skills, including nature-writing, nature-polishing, nature-response, nature-reader, and nature-paper2ppt. Do not invoke it as a standalone user workflow. Load only the specific core or journal-format file requested by another Nature skill.

Draft, restructure, or plan Nature-style manuscript sections and initial-submission materials from author-provided claims, results, figures, notes, or Chinese drafts. Use for abstracts, introductions, related work, methods, Results or experiments, discussions, conclusions, titles, full manuscript arguments, and first-submission packages such as cover letters, title pages, highlights, author contributions, availability or declaration text, and reviewer suggestions. Also use to classify Results...

Publication-style figure authoring for omics / bioinformatics results. Use whenever the user asks for a (single) plot, figure, or chart from analysis results or a data table — volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA / UMAP / t-SNE, Kaplan–Meier. The figures are drawn with matplotlib / seaborn; this skill supplies the shared style and copy-paste recipes so every figure looks like one consistent, journal-ready system. To combine se...

Flags irreversible decisions before commit. Use for data models, infra, auth boundaries, API contracts, event schemas, CI/CD.

Web page change detection, availability tracking, and RSS feed generation. Use to monitor changes, downtime, or make a feed.

Designs PDF reports and proposals from HTML with previews and branding. Use to create, export, or securely upload a PDF.

Generates CLAUDE.md project memory files that transfer institutional knowledge. Use when setting up projects or onboarding.

Generates LESSONS.md files capturing institutional knowledge and failures. Use when closing out projects or investigations.

This skill should be used when the user asks to \"optimize a prompt\", \"improve prompt performance\", \"design a prompt template\", \"write better prompts\", \"debug prompt issues\", \"use chain-of-thought\", \"structured prompting\", \"few-shot prompting\", or wants to apply advanced prompt engineering patterns for production LLM applications.

"End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools.

"Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite ...

"Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design.

Python design patterns including KISS, Separation of Concerns, Single Responsibility, and composition over inheritance. Use this skill when designing a new service or component from scratch and choosing how to layer responsibilities, when refactoring a God class or monolithic function that has grown too large, when deciding whether to add a new abstraction or live with duplication, when evaluating a pull request for structural issues like tight coupling or leaking internal types, when choosin...

Python data pipelines with modular architecture. Use for content workflows, batch jobs, or Google Sheets/Drive integration.

Build Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.

"Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers.

Secure authentication patterns (OWASP, NIST). Use for login, registration, password reset, sessions, JWT, OAuth, MFA, passkeys.

Pre-deployment security audit organized by OWASP Top 10. Use when reviewing code before shipping or going to production.

First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with \"file not found\" or \"modal: command not found\", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.

Social media monitoring, narrative tracking, and OSINT. Use when tracking viral spread, coordinated campaigns, or account vetting.

"Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation.

Verify sources, claims, images, video, documents, interviews, and synthetic media with SIFT and a durable evidence trail. Use before relying on uncertain material.

Spring Security best practices for authn/authz, validation, CSRF, secrets, headers, rate limiting, and dependency security in Java Spring Boot services.

Thread-safe data persistence in Swift using actors — in-memory cache with file-backed storage, eliminating data races by design.

Protocol-based dependency injection for testable Swift code — mock file system, network, and external APIs using focused protocols and Swift Testing.

AI-assisted video editing workflows for cutting, structuring, and augmenting real footage. Covers the full pipeline from raw capture through FFmpeg, Remotion, ElevenLabs, fal.ai, and final polish in Descript or CapCut. Use when the user wants to edit video, cut footage, create vlogs, or build video content.

Guide for implementing 1Password secrets management - CLI operations, service accounts, Developer Environments, and Kubernetes integration. Use when retrieving secrets, managing vaults, configuring CI/CD pipelines, integrating with External Secrets Operator, managing Developer Environments, or automating secrets workflows with 1Password.

Deploy Azure Landing Zones using the ALZ Accelerator with AVM (Azure Verified Modules). Use this skill whenever the user mentions Azure Landing Zones, ALZ, Azure landing zone accelerator, AVM modules for landing zones, deploying management groups, hub-and-spoke networking, Virtual WAN, platform landing zones, or asks about Bicep vs Terraform for Azure infrastructure. Also trigger when the user wants to bootstrap CI/CD for Azure platform deployment, set up management groups hierarchy, or deplo...

Advanced ArgoCD operations beyond the core CLI/API — multi-cluster ApplicationSet generators, automated image updates, new-cluster bootstrapping, and workload onboarding via templated ApplicationSets. USE WHEN working with ApplicationSet CRDs (list, cluster, git, matrix, merge, SCM, pull request, plugin generators), configuring ArgoCD Image Updater (semver/digest/newest-build update strategies + git write-back), bootstrapping a new Kubernetes cluster into a multi-repo GitOps setup, registerin...

Complete ArgoCD cluster bootstrapping skill for diagnosing sync failures, creating root Applications (app-of-apps), curating ApplicationSets via Kustomize, and resolving missing CRD dependencies. USE WHEN argocd bootstrap OR app-of-apps pattern OR root application OR applicationset gitops management OR argocd sync failed missing CRD OR kustomize applicationset curation OR argocd cluster onboarding.

Manage ArgoCD Image Updater configuration, drift resolution, and ImageUpdater CRDs. USE WHEN argocd image updater, image update drift, ImageUpdater CRD, extraObjects helm, environment-scoped image updates, argocd-image-updater troubleshooting.

Shell history management with Atuin. Use when configuring shell history, setting up history sync, searching command history, importing history from other shells, troubleshooting atuin issues, or optimizing history workflows. Covers installation, sync setup, search modes, statistics, and self-hosting.

Azure AKS Agentic CLI - AI-powered troubleshooting and insights tool for Azure Kubernetes Service. Use when diagnosing AKS cluster issues, getting cluster health insights, troubleshooting networking/storage/security problems, or analyzing cluster configuration with natural language queries.

Use when exporting existing Azure resources to Terraform using aztfexport. Triggers on aztfexport, Azure import to Terraform, export Azure resource, bring Azure under Terraform management, reverse-engineer Azure infrastructure, bootstrap IaC from live Azure resources. Covers resource, resource-group, and query modes.

Azure AD OAuth2/OIDC SSO integration for Kubernetes applications. Use when implementing Single Sign-On, configuring Azure AD App Registrations, restricting access by groups, or integrating tools (DefectDojo, Grafana, ArgoCD, Harbor, SonarQube) with Azure AD authentication.

Install and connect the Azure Cost Management App (by Microsoft Corporation) in Power BI Service via browser automation. Use this skill whenever the user mentions installing, deploying, connecting, or configuring the Azure Cost Management template app in Power BI, or when they want to connect Power BI to their EA (Enterprise Agreement) enrollment for cost visibility. Also triggers when the user says "connect your data" on the Cost Management App, wants to set up EA cost data in Power BI, or n...