DevOps e Infra

Use to evaluate a service or feature against Downe's 15 principles of good services.

Execute ENCODE ChIP-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Use when users need to process ChIP-seq data following ENCODE standards, run peak calling with MACS2, perform IDR analysis, or generate signal tracks. Trigger on: ChIP-seq pipeline, run ChIP-seq, process

Execute CUT&RUN processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing CUT&RUN or CUT&Tag data, an alternative to ChIP-seq with lower background. Trigger on: CUT&RUN pipeline, CUT&Tag, SEACR, Henikoff, targeted chromatin, pA-MNase, process CUT&RUN.

Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification

Use when real user interviews aren't possible (solo/hobby/dogfood projects) but persona work is still needed. Enforces epistemic discipline: adversarial spectrum, pre-committed stop conditions, speculation tagging. NOT a substitute for /mycelium:user-interview when real users are available.

Battle-tested skills and hooks for Claude/Codex/Gemini/Pi.

Generate interactive Three.js canvases in six modes: narrative particle phase cycles, WebGPU spinner/loaders, infinite gallery tunnels, animated glTF specimens, vinyl showcase with webcam reflection, glass hero sections with physically-accurate refraction/dispersion/iridescence. Ships a reusable Phosphor Vigil FX post-processing module (CRT composite, scanlines, chromatic aberration). Self-contain

Systematically challenge current assumptions before major decisions. Counters confirmation bias, groupthink, and overconfidence.

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific as

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts, and Python requirements. Use when the user needs to set up a bioinformatics workstation, install tools for a specific as

Recreate grainient.supply's 16 dark-mode visual effects as single-file HTML pages: WebGL shader gradients, vignette overlays, 9-layer box shadows, smooth scroll, spring animations, hover-zoom, ticker marquees, glassmorphism, 3D card flips, bento grids, gradient CTAs. Dark-mode-first with lime green (#C2F13C) accent. Triggers on grainient effects, dark-mode landing page, cinematic depth, glow effec

Execute ENCODE Whole Genome Bisulfite Sequencing (WGBS) pipeline from FASTQ to methylation calls. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing WGBS/bisulfite-seq data, calling methylation levels, generating bedMethyl files. Trigger on: WGBS pipeline, bisulfite sequencing, methylation calling, DNA methylation pipeline, bismark, bwa-meth,