LLM Mart Basic

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting t

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting chan

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preproces

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or

Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when wor

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR again

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 datase

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstruct

Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inve

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially express

Build complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple

Read and write genomic alignment and variant files in Python with pysam (htslib bindings) — SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, plus region extraction and per-base coverage/pileup. Use when scripting NGS data-processing pipelines that parse, filt

Runs 16S/ITS amplicon (microbiome) analysis with the QIIME 2 distribution (2026.7; the "amplicon" distribution was renamed "qiime2" in 2026.4) in the correct order: manifest import, cutadapt trim-paired primer removal BEFORE dada2 denoise-paired (trunc-len chosen from the demux q

Generate de-novo protein backbones with RFdiffusion (Watson 2023) — a diffusion model for unconditional monomer generation, motif scaffolding, binder design against a target, and symmetric oligomers. Use when generating a new protein backbone from scratch, scaffolding a functiona

Quantifies bulk RNA-seq transcript abundance with salmon 2.x (the Rust rewrite; selective alignment or --sketch) and kallisto (v0.52.0, kb-python workflow), builds a decoy-aware gentrome index, runs quant with --gcBias -l A, then imports estimates via tximport/tximeta with a tx2g

Run the standard single-cell RNA-seq analysis pipeline with Scanpy on AnnData — QC filtering, normalization, dimensionality reduction (PCA, UMAP, t-SNE), Leiden/Louvain clustering, marker/differential expression, PAGA trajectories, and plotting. Use when analyzing scRNA-seq data

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretraine

Fourteen posts of being wrong in production, compressed to checkboxes

Healthy nodes, a quiet network, 300 restarts in three days, and a latency budget measured in milliseconds

Discovery worked. Ping worked. Every TCP connection timed out, and later the tunnel only worked when someone had a terminal open.

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Instrument services with structured logging, Prometheus metrics, and OpenTelemetry tracing. Build Grafana dashboards, write Prometheus alerting rules, run k6 load tests, and plan infrastructure capacity.

Generate, test, validate, explain, and debug OPA (Open Policy Agent) Rego policies and Conftest configurations. Covers deny/warn/violation rules, unit tests, regal linting, conftest fmt, namespace design, input shape analysis, and GitHub Actions integration. Use when asked to "write a policy", "test a rego file", "validate policies", "explain this rego", or "why is my policy not firing".

OpenShift SCC diagnosis and hardening, Route TLS patterns, OpenShift GitOps app delivery, and cluster upgrade validation.

Comprehensive PR review across six dimensions — cost impact, environment drift, ownership gaps, SOC 2 compliance, deprecated API / version hygiene, and rollback feasibility. Each mode inspects the diff and current file state, reports findings with severity, and recommends concrete fixes. Use when preparing a PR for merge, conducting a pre-deployment readiness check, or performing a post-merge risk assessment.

Production-readiness preflight check for a directory, repo, or single file. Auto-detects file types (Kubernetes manifests, Terraform, GitHub Actions workflows, Helm values/charts, Flux Kustomizations/HelmReleases, Dockerfiles, shell scripts) and applies type-specific checks across the whole scope. Returns a per-file summary table and aggregated verdict. Use before deploying, merging, or applying a folder of config. For PR diffs spanning multiple files use /platform-skills:pr-review instead. For deep Helm chart work use /platform-skills:helmchart instead.

Apply product thinking to platform work — DevEx audits, friction analysis, RFC/ADR drafting, incident communication, post-mortems, capacity planning, cost optimisation, and platform health review.

Generate renovate.json covering all dependency file types used in a repo, emit a GitHub Actions workflow that validates renovate.json on every PR, or generate a pre-commit hook for local validation.

Detect and respond to in-container threats at the syscall level using Falco (eBPF-based, CNCF, open-source, no license cost). Covers Falco installation on EKS/GKE with eBPF driver, custom rule authoring, alert routing via Falcosidekick, rule debugging, and bridging Falco runtime signals to Kyverno admission enforcement. Use when asked to "detect privilege escalation in containers", "set up runtime threat detection", "write a Falco rule", "route Falco alerts to Slack", or "debug why my Falco rule is not firing".

Secrets strategy, External Secrets Operator scaffolding, Sealed Secrets seal/rotate/backup, rotation runbooks, and Kubernetes-side secrets audit.

Bootstrap and operate a self-improving agent workspace. Scaffolds .learnings/ and memory/ directories, captures errors and learnings during a session, detects recurring patterns, recalls verified lessons, and promotes stable entries to scoped rule files (.claude/rules/ or ~/.claude/rules/). Also implements the Proactive Agent pillars — WAL protocol, working buffer, SESSION-STATE, daily notes, VBR, VFM scoring, ADL decision logic, heartbeat, and reverse prompting. Use when asked to "remember this lesson", "set up agent memory", "log that error", "what did we learn about X", "promote learnings", "revoke that rule", "capture session state", or "enable proactive mode".

Scaffold a multi-agent AI setup for any repo. Scans the codebase, interviews the developer, generates agent configs for whichever AI tools the repo uses (Copilot, Claude Code, Cursor, Codex, Windsurf). Use when asked to "set up agents", "scaffold Copilot agents", or "create an AGENTS.md".

Secure the software supply chain from source to running container. Covers Cosign keyless image signing (Sigstore/Rekor), SBOM generation and attestation (Syft), vulnerability scanning with severity gates (Trivy/Grype), SLSA Level 2 provenance, and Kyverno/OPA admission enforcement. All open-source, no license cost. Use when asked to "sign my image", "generate an SBOM", "scan for CVEs", "attest build provenance", "enforce image signatures in Kubernetes", or "implement SLSA".

Runs through the full Terraform validation pipeline — fmt, validate, tflint, security scan — and reviews a module or plan for blast radius, IAM risk, and state impact.

Triages a PR comment — from a bot (Copilot, CI) or a human reviewer. Routes to the `triage_helper.py` helper for identity checks, thread snapshotting, isolated-worktree fixes, and publish/reply/resolve mechanics; you classify the finding and apply a justified fix. `--dry-run` is fully read-only (investigation and a printed plan, zero mutations). `--no-resolve` runs the full fix/reply workflow but never resolves a thread. Run from inside the repo.

Scan container images, filesystems, git repos, and existing SBOMs for CVEs, secrets, and license violations using Trivy. Covers local CLI, CI severity gates with SARIF upload, and continuous monitoring via Trivy Operator (Flux HelmRelease). Use when asked to "scan my image", "check for CVEs", "scan this repo for secrets", "scan an SBOM", or "set up continuous cluster vulnerability monitoring". IaC misconfig → /platform-skills:checkov. Admission posture → /platform-skills:kyverno. Image signing/SBOM generation → /platform-skills:supply-chain.

Audit GitHub Actions workflows, composite actions, Dependabot configs, and pre-commit configs for security findings using zizmor — template injection, credential persistence, unpinned uses, over-broad permissions, impostor commits. Covers local CLI, auto-fix, zizmor.yml policy, severity-based CI gates, SARIF upload, and pre-commit. Use when asked to "audit my workflows", "run zizmor", "is this workflow safe", "check for template injection", "pin my actions", or "set up a zizmor CI gate". Workflow syntax and shell errors → /platform-skills:github-actions (actionlint). IaC misconfig → /platform-skills:checkov. Image and dependency CVEs → /platform-skills:trivy. Keeping SHA pins fresh → /platform-skills:renovate.

반복 작업을 `/이름` 으로 호출. 파일명 = 커맨드 이름(`fix-issue.md` → `/fix-issue`).

이슈 #$ARGUMENTS 를 처리한다(이슈 우선 워크플로):

AGENTS.md 생태계(rules·memory·agents·skills·commands·workflows)의 연결 구조를

이슈/기획서 기준 SDLC 한 사이클(이슈→개발→테스트→검증→PR/MR)을 사람 개입 없이 자동 실행.

AI coding platform for teams

AI Multi-Agent Framework in .NET

Production-ready code examples for Telnyx AI Communications Infrastructure — Voice AI, SMS, SIP, and IoT APIs

UltraGameStudio - AI coding agent for game development: engine workflows, gameplay code, and asset generation.

🦞 ResearchClawBench: Evaluating AI Agents for Automated Research from Re-Discovery to New-Discovery

The context-aware model router that learns & adapts to your long-horizon coding agent workflows. Lightweight & extensible, works with any harnesses, any models,…

Open-source sandboxes where coding agents build and deploy. Spin up isolated environments where Claude Code, Cursor, and other agents code and deploy software.

Native desktop UI for Claude Code with orchestration, streaming, background agents, and multi-provider support. Built with Tauri + React.

OpenCode mobile client via Telegram: run and monitor AI coding tasks from your phone while everything runs locally on your machine. Scheduled tasks support.

Terminal session manager for AI coding agents. One TUI for Claude, Gemini, OpenCode, Codex, and more.

Exposes internet search tools for use by LLM-backed Assist in Home Assistant

Templates and workflow for generating PRDs, Tech Designs, and MVP and more using LLMs for AI IDEs

Versus Incident is the self-hosted AI SRE agent. It learns what your system normally look like and escalates only what is new or unexpected issues — routing to…

Browser-native side panel for Hermes Agent — connect web context to your local Hermes runtime.

Agentic-friendly CLI generator for APIs: turn Swagger, OpenAPI, and google.api.http protos into single-binary CLIs with catalogs and generated Skills.

Open-source agent platform for Global × China enterprises — wire every system through one agent core. Self-hosted, any LLM.

Official python implementation of UTCP. UTCP is an open standard that lets AI agents call any API directly, without extra middleware.

An agent small enough to run anywhere. A minimal agentic runtime in C — ~380 lines, 54KB binary, ~2MB RAM. A skill file + an LLM + a shell loop, no framework.

AgentiLoop Agent! An Autonomous Agentic Agent for Mac, and exclusive Apple only harnesss. Suppprtd automation, scripting, coding, build anything and more. Power…

微信公众号 AI 运营助手 | 选题、写稿、审稿、排版、配图、发布全流程 Skill，支持 OpenClaw / Claude Code / Cursor / Codex