「md」の検索結果

Repair and verify cross-references between SKILL.md files after a skill is created, renamed, removed, or restructured. Ensures every skill that calls another skill references the correct name, and every skill that is called has accurate "Called by" context. Load after universal-skill-creator creates a skill, after improve-skills completes a cycle, after a skill is renamed or removed, or when the user asks to fix cross-references, sync skill links, repair broken skill references, update skill cross-links, check skill references, or "are cross-links correct".

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Sync the live ~/.claude global config (settings.json, CLAUDE.md, statusline.ts, own skills, skills.sh lock file) into this git backup repo, then commit. Allowlist-based so credentials, history, and project transcripts are never copied. Use when the user says "sync my claude config", "back up .claude", "update the .claude repo", or runs "/sync-claude".

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These are instructions for creating design philosophies - aesthetic movements that are then EXPRESSED VISUALLY. Output only .md files, .pdf files, and .png files.

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Important: Before you begin, fill in the generatedBy property in the meta section of .actor/actor.json. Replace it with the tool and model you're currently using, such as "Claude Code with Claude Sonnet 4.5". This helps Apify monitor and improve AGENTS.md for specific AI tools and models.

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Senior embedded software engineer specializing in firmware and driver development for ARM Cortex-M microcontrollers (Teensy, STM32, nRF52, SAMD).

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Algorithmic philosophies are computational aesthetic movements that are then expressed through code. Output .md files (philosophy), .html files (interactive viewer), and .js files (generative algorithms).

日本語の概要は準備中です。原文の説明を表示しています。

Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

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Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.

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Analyzes species-environment relationships with constrained ordination (CCA, RDA, db-RDA), variance partitioning, indicator species (indicspecies IndVal.g group-equalized), PERMANOVA paired MANDATORILY with PERMDISP (Anderson & Walsh 2013; dispersion confounds centroid tests), Joint Species Distribution Models (HMSC, sjSDM, gjam) with explicit rejection of "residual covariance equals biotic interaction", phylogenetic community ecology (SES_MPD/MNTD), trait-environment via RLQ + fourth-corner with corrected modeltype=6 (Dray 2014), bipartite network metrics (NODF, modularity) with curveball null (Strona 2014), and Mantel-test replacements (dbRDA, GDM) for spatial data. Use when testing how environmental gradients structure communities, identifying habitat indicator taxa, partitioning variance among predictors, deciding whether PERMANOVA significance is location vs dispersion, picking among HMSC/sjSDM/gjam, or replacing Mantel tests for landscape data.

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Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.

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Performs alchemical free-energy calculations including relative binding free energy (RBFE / FEP+) and absolute binding free energy (ABFE) via OpenFE, FEP+, GROMACS, AMBER pmemd, and OpenMM with explicit lambda window scheduling, soft-core potentials, REST2 enhanced sampling, MBAR/BAR analysis, and cycle closure validation. Compares ML alternatives (Boltz-2 affinity, DeepDock). Use when ranking analogs by binding affinity beyond docking accuracy, performing prospective lead optimization, or validating SAR predictions.

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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Detects aberrant splicing in single rare-disease patients vs a control panel using FRASER 2.0 (Bioconductor; Beta-binomial autoencoder on Intron Jaccard Index, default delta cutoff 0.1, q hyperparameter), OUTRIDER (gene-level outlier expression via autoencoder denoising), LeafcutterMD (Dirichlet-multinomial outlier mode of LeafCutter for annotation-free junctions), and DROP (Snakemake pipeline integrating FRASER2 + OUTRIDER + monoallelic expression for clinical diagnostics). The statistical model is fundamentally different from differential splicing — single-sample-vs-cohort outlier detection rather than two-group comparison. Standard tool in EU rare-disease (Solve-RD) and NIH UDN programs. Use when applying RNA-seq to undiagnosed Mendelian disease, validating predicted splice variants in clinical samples, or detecting cryptic splicing in disease tissue.

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集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.

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Use when a carrier asks about fuel-card vendor selection (Comdata, EFS, WEX, RTS, Pilot Flying J, Love's Connect), discount levels, fraud control, driver authorization PINs, IFTA reporting features, cash advance, money codes, or how the card fits into payroll/settlement workflows.

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One-time recovery when a shared checkout has drifted far from GitHub main: hundreds ahead/behind, stacked worktrees and PRs, a dirty tree nobody owns. Use when tempted to reset or force-push. NOT for the ordinary 30-minute release loop (operations/INTEGRATION_MAINTAINER.md).

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Adding a file type or upgrading any of its capability slots in the files feature (preview, edit, thumbnail, grid card, info, share, versions, conversion, diff, rail panel). Use when supporting a new extension or MIME type, building a previewer, touching FILE_TYPES, PreviewKind, FilePreview.tsx, EDITABLE_KINDS, or surfaces/single-file/, or working the FILE_SURFACES.md wishlist.

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The quick interview that captures a Domain's or major Feature's minimal (go-live) and final vision verbatim into its VISION.md. Use when a node shows VISION MISSING, a registry domain is ratified without a vision, gap analysis lacks a go-live bar, or on /domain-vision-interview <domain>.

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Create a new find-XXXX preprocessor Python script from scratch (no existing SKILL.md), add configs/<GAMEVER>.yaml skill and symbol entries. Covers xref-string-based and LLM_DECOMPILE-based discovery patterns. Use when a GitHub issue or user instruction specifies a new function to find.

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Create and manage teams of specialized AI agents that work together on tasks. Use when setting up multi-agent workflows, agent squads for content/marketing/research pipelines, configuring heartbeat-based agent coordination, or managing agent personalities via SOUL.md files. Enables orchestration of multiple OpenClaw sessions as a coordinated team with shared task systems (Linear, Trello, etc.).

日本語の概要は準備中です。原文の説明を表示しています。

Generates README.md files for PHP projects. Creates structured documentation with badges, installation, usage, and examples.

日本語の概要は準備中です。原文の説明を表示しています。

Generates CHANGELOG.md files following Keep a Changelog format. Creates version history documentation.

日本語の概要は準備中です。原文の説明を表示しています。

Generates ARCHITECTURE.md files for PHP projects. Creates layer documentation, component descriptions, and architectural diagrams.

日本語の概要は準備中です。原文の説明を表示しています。