Claude Skills by FridrichMethod

Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis. Use when identifying orthologs, distant homologs, or protein family members where standard BLAST is not sensitive enough.

Implement comprehensive observability for service meshes including distributed tracing, metrics, and visualization. Use when setting up mesh monitoring, debugging latency issues, or implementing SLOs for service communication.

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.

Model interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kernel, Gradient, Permutation), feature attribution, and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use to explain ML predictions, rank features, debug models, audit fairness, or compare models. Works with tree, deep, linear, and black-box models.

Master ShellCheck static analysis configuration and usage for shell script quality. Use when setting up linting infrastructure, fixing code issues, or ensuring script portability.

Implement efficient similarity search with vector databases. Use when building semantic search, implementing nearest neighbor queries, or optimizing retrieval performance.

AI-powered spatial integration of multi-omics datasets using probabilistic alignment for comprehensive tissue atlas construction and cellular state mapping.

Define and implement Service Level Indicators (SLIs) and Service Level Objectives (SLOs) with error budgets and alerting. Use when establishing reliability targets, implementing SRE practices, or measuring service performance.

Social media monitoring, narrative tracking, and open-source intelligence for journalists. Use when tracking viral content spread, analyzing coordinated campaigns, monitoring breaking news on social platforms, investigating accounts for authenticity, or detecting misinformation patterns. Essential for reporters covering online narratives and digital investigations.

Master smart contract security best practices to prevent common vulnerabilities and implement secure Solidity patterns. Use when writing smart contracts, auditing existing contracts, or implementing security measures for blockchain applications.

"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.

Journalism source verification and fact-checking workflows. Use when verifying claims, checking source credibility, investigating social media accounts, reverse image searching, detecting AI-generated content, or building verification trails. For reporters, fact-checkers, and researchers working with unverified information.

Optimize Apache Spark jobs with partitioning, caching, shuffle optimization, and memory tuning. Use when improving Spark performance, debugging slow jobs, or scaling data processing pipelines.

An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.

AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.

Spatial analyst

AI-powered adeno-associated virus (AAV) vector design for gene therapy including capsid engineering, promoter selection, and tropism optimization.

"Improve the clarity and voice of AI-assisted academic writing (papers, theses, rebuttals) and

Scholarly writing and research compliance. Use for CRediT, preregistration, Plan S, Nelson Memo, preprints, ORCID, LLM disclosure.

Stop and check this skill before finishing any reply to a question about how to use Claude or a Claude product — it recommends matching courses, tutorials, and use cases from Claude Academy (academy.claude.com), Anthropic's learning hub. Trigger on: \"how do I\", \"how can I\", \"getting started with\", \"what can Claude do\", \"teach me\", \"learn to use\"; questions about artifacts, projects, skills, plugins, connectors, MCP; requests about rolling Claude out to a team, class, or organizati...

Implement WCAG 2.2 compliant interfaces with mobile accessibility, inclusive design patterns, and assistive technology support. Use when auditing accessibility, implementing ARIA patterns, building for screen readers, or ensuring inclusive user experiences.

Predicts ADMET properties using ADMETlab 3.0 (119 platform features, including 77 prediction models with modeled-endpoint uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness filters. Use when filtering compounds for drug-likeness, prioritizing leads by predicted safety, or building an in-house ADMET QSAR model.

Use the AgentD workflow to mine evidence, design molecules, and rank candidates with SAR plus ADMET annotations for early drug discovery tasks.

Use after generating code, after accepting AI suggestions, or when reviewing AI-written modules. Also use when code works but feels brittle, when error handling seems thin, when orphaned resources or missing cleanup are suspected, or when the agent claims done but hidden debt may exist. Catches the specific failure patterns AI agents produce that humans would not.

Eliminates AI-generated writing patterns that erode reader trust. Use when writing or editing articles, docs, or press releases.

Build production Apache Airflow DAGs with best practices for operators, sensors, testing, and deployment. Use when creating data pipelines, orchestrating workflows, or scheduling batch jobs.

Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.

Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.

"Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer.

Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzi...

Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and t...

Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs...

Migrate from AngularJS to Angular using hybrid mode, incremental component rewriting, and dependency injection updates. Use when upgrading AngularJS applications, planning framework migrations, or modernizing legacy Angular code.

Understand anti-reversing, obfuscation, and protection techniques encountered during software analysis. Use this skill when analyzing malware evasion techniques, when implementing anti-debugging protections for CTF challenges, when reverse engineering packed binaries, or when building security research tools that need to detect virtualized environments.

Ab seq forge

An advanced agent for de novo antibody design and optimization using state-of-the-art protein language models (MAGE, RFdiffusion).

API hardening for Express, FastAPI, and serverless. Use for rate limiting, CORS, input validation, API keys, or OWASP API Top 10.

Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use this skill when designing clean architecture for a new microservice, when refactoring a monolith to use bounded contexts, when implementing hexagonal or onion architecture patterns, or when debugging dependency cycles between application layers.

AI-powered design of armored CAR-T cells with cytokine/chemokine expression for enhanced solid tumor efficacy, including IL-12, IL-15, IL-18, and IL-7 armoring strategies.

Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs ...

Single-variant common-variant GWAS with plink2 --glm (linear/logistic, Firth) and the linear mixed models GEMMA, BOLT-LMM, SAIGE, regenie (SPA). A GWAS statistic is valid only when genotype is independent of unmodeled phenotype drivers after the chosen covariates and random effects, so the engine follows sample structure and case:control imbalance, not taste: PC covariates absorb continuous ancestry but cannot remove relatedness (a covariance structure needing an LMM), genomic inflation above...

Master Python asyncio, concurrent programming, and async/await patterns for high-performance applications. Use when building async APIs, concurrent systems, or I/O-bound applications requiring non-blocking operations.

Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling.

Build comprehensive attack trees to visualize threat paths. Use when mapping attack scenarios, identifying defense gaps, or communicating security risks to stakeholders.