LLM Mart Basic

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,

Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger o

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinica

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

Guide for integrating GTEx tissue expression data with ENCODE regulatory elements. Use when users need to check if a gene is expressed in a tissue, correlate regulatory elements with expression, or validate ENCODE findings against GTEx. Trigger on: GTEx, tissue expression, gene e

Guide for integrating NHGRI-EBI GWAS Catalog associations with ENCODE regulatory data. Use when users need to find GWAS variants in ENCODE peaks, connect regulatory elements to disease associations, or prioritize functional variants using ENCODE annotations. Trigger on: GWAS, gen

Build comprehensive chromatin contact maps by aggregating Hi-C loop calls (BEDPE) across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "what regions are in 3D contact in my tissue?" by creating a union catalog of chromatin loops. Handles resolut

Build comprehensive histone mark maps by aggregating narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is this histone mark present in my tissue?" by combining peak calls from multiple studies into a union peak set with

Plan and execute integrative analysis combining multiple ENCODE experiments for cross-dataset or multi-omic workflows. Use when the user wants to combine experiments, perform cross-dataset comparison, multi-omic integration, peak overlap analysis, differential binding, signal cor

Guide for using JASPAR transcription factor binding profiles with ENCODE ChIP-seq data. Use when users need to find TF binding motifs in ENCODE peaks, validate ChIP-seq targets with known motifs, or scan regulatory regions for TF binding potential. Trigger on: JASPAR, motif datab

Convert genomic coordinates between assembly versions (GRCh37/hg19 to GRCh38/hg38, mm9 to mm10). Guides UCSC liftOver for BED files, CrossMap for VCF/bigWig, and handles unmapped regions with provenance logging.

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.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

Analyze git diffs or staged changes and generate conventional commit messages that explain WHY a change was made. Supports auto-detecting type and scope, intelligent file staging, and interactive overrides. Use when asked to "write a commit message", "generate a commit", "describe my changes", "commit this", "summarize my diff", or "/commit".

SOC 2 compliance for Terraform — gap analysis, control implementation, evidence collection, and remediation guidance mapped to SOC 2 Trust Services Criteria.

Generate, review, secure, and test composite GitHub Actions following best practices — full repo scaffold, interview-driven generation, PR creation on existing repos, SHA pinning, secrets-as-inputs, job summaries, and actionlint validation.

Set up and troubleshoot Datadog — Agent deployment on Kubernetes, APM instrumentation, Log Management, Monitors, Dashboards, SLOs, Synthetic tests, and live incident investigation using the Datadog MCP server. Covers Terraform-managed Datadog resources.

Structured platform troubleshooting — classifies the problem layer, collects evidence, forms a root-cause hypothesis, and proposes a fix with validation and rollback steps.

Generate, format, and validate code documentation — docstrings, JSDoc, OpenAPI/Swagger specs, documentation sites, and developer guides.

Measure, benchmark, instrument, and debug DORA metrics (Deployment Frequency, Lead Time for Changes, Change Failure Rate, MTTR) for production engineering teams. Covers GitHub Actions instrumentation, Prometheus recording rules, Grafana dashboards, incident source integration, SaaS tool selection, and anti-pattern detection. Use when asked to "instrument DORA metrics", "benchmark our deployment frequency", "why is my MTTR data missing", or "generate a DORA dashboard".

Deploy and configure Dynatrace — OneAgent Kubernetes Operator, code-level instrumentation, Log Monitoring, custom metrics, SLOs, Dashboards, anomaly detection, Davis AI, and live incident investigation using the Dynatrace MCP server. Covers Terraform-managed Dynatrace resources.

FluxCD entry point — routes to the right workflow based on what you need. Live cluster issue → structured 5-workflow debug trace. Repo health check → 6-phase audit (discovery, validation, API compliance, best practices, security). Helm chart review → helmchart. Starts by asking one question to confirm the right mode.

Design, review, secure, and debug GitHub Actions workflows — reusable workflows, OIDC federation, SHA pinning, token scoping, promotion orchestration, and CI failure diagnosis.

Flux CD and Argo CD — two modes. debug: five structured debug workflows for live clusters (installation, source, HelmRelease, Kustomization, ResourceSet) producing a five-section report. audit: six-phase read-only repo analysis (discovery, validation, API compliance, best practices, security) producing a prioritised Critical/Warning/Info report.

Scaffold, lint, review, security-audit, test, and upgrade-verify Helm charts. Runs an interactive interview to build production-ready charts from scratch. Covers chart structure, values design, schema validation, kubeconform, helm diff, and multi-environment scaffolding. Use when asked to "create a helm chart", "lint my chart", "review my helm chart", "check helm security", "generate values schema", "run helm diff", or "add helm tests".

Design, install, debug, review, plan capacity, audit scaling history, migrate from Cluster Autoscaler, and upgrade Karpenter v1.x on EKS. Covers NodePool, EC2NodeClass, NodeClaim, Spot diversity, disruption strategy, Pod Identity/IRSA, interruption queue, private clusters, AMI rotation, and GitOps integration. Use when asked to "set up Karpenter", "debug why nodes aren't provisioning", "review my NodePool", "what would Karpenter provision for this workload", "why did this node terminate", "migrate from CA", or "upgrade Karpenter".

Design, debug, and review KEDA ScaledObject/ScaledJob autoscaling. Covers all major scalers (Prometheus, SQS, Kafka, Redis, Cron, HTTP Add-on, Azure Service Bus), TriggerAuthentication, scaling lifecycle tuning, GitOps integration, and troubleshooting. Use when asked to "add KEDA autoscaling", "debug why my ScaledObject isn't scaling", "review my KEDA config", or "generate a ScaledObject for <trigger>".

Find, live-validate, map the blast radius of, and revoke leaked secrets with Kingfisher (MongoDB) — across a local repo, Git history, a GitHub/GitLab/Bitbucket org, S3/GCS, Docker images, Slack, Jira, Confluence, Teams, or Postman. Covers local CLI scanning, direct validate/revoke without a scan, baseline management (track only new secrets), kingfisher.yaml policy, CI diff-scan gates, and pre-commit/Husky hooks. Use when asked to "scan for secrets", "is this key still live", "what can this credential reach", "revoke this token", "did we leak a secret", or "block new secrets in CI". Pattern-only secret scan bundled with a CVE pass → /platform-skills:trivy. Secrets-context safety in workflow YAML → /platform-skills:zizmor. Storing/rotating secrets inside the cluster → /platform-skills:secrets.

Cluster baseline scaffolding, RBAC diagnosis and generation, workload hardening, and structured pod/scheduling debug for plain Kubernetes across all distributions.

Generate, test, audit, debug, and migrate Kyverno policies using the new CEL-based policy types (ValidatingPolicy, MutatingPolicy, GeneratingPolicy, ImageValidatingPolicy — all apiVersion policies.kyverno.io/v1). Covers matchConstraints, matchConditions, CEL validations/mutations, generator.Apply(), Audit→Deny promotion, PolicyException, kyverno-cli testing, and migration from legacy ClusterPolicy or PodSecurityPolicy. Use when asked to "write a Kyverno policy", "test a ValidatingPolicy", "audit my cluster for violations", "why is my policy not firing", or "migrate from ClusterPolicy".

Linkerd-specific diagnostics — mTLS verification, proxy injection issues, authorization policy debugging, traffic management, and multi-cluster connectivity problems.

Linux administration and networking diagnostics — DNS, load balancing, VPCs, kernel tuning, and connectivity troubleshooting.

MCP server and client development — scaffold, implement tools/resources/prompts, validate schemas, debug protocol compliance, and deploy with auth and rate limiting.

An open-source, privacy-first, self-hosted knowledge workspace where humans and AI agents work together 开源、隐私优先、自托管的知识工作空间，让人与智能体在此协作

Scale computer-use 2.0 with open-source drivers, cross-OS fleets, and benchmarks for training, evaluation, and data generation.

The go-to web for your AI coding agent — local-first search, fetch, crawl & research over MCP. No API keys, no cloud, $0/query. Public beta.

Transform and optimize your markdown documentation for Large Language Models (LLMs) and RAG systems. Generate llms.txt automatically.

合乎周礼：DeepSeek-powered Zhouli-style Chinese translator, web app, and distributable Skill package.

This is a fork of the https://dockbox.dev project I made

🏆 Curated, ranked list of AI agent harnesses (100+) — plus an MCP server, llms.txt & JSON so agents can recommend them too. Rescored weekly.

A Python framework for modular, self-contained skill management for machines.

ADHD — a skill for coding agents. Tree-of-thought with pruning, built on the Claude & Codex Agent SDK. Fans out parallel divergent thoughts under different cogn…

AI Agent 驱动的开源可自部署视频工作台：将小说与剧本转为角色、场景、道具资产、分镜、视频和剪映草稿，支持跨镜头一致性、多供应商与费用追踪 | Self-hosted AI video workspace for stories, storyboards and short-form video producti…

DeepSeek Harness Desktop App: a local AI desktop workspace for DSH Sessions, projects, files, web research, plugins, and Office artifacts.

Autonomous Offensive Security, Bug Bounty & Red Teaming Agent Framework powered by Hermes Agent, specialized reasoning skills, and multi-model LLM orchestration…

⌥ Coding agent with the IDE wired in

Supercharge AI Agents, Safely

X (Twitter) Scraper API and X API Alternative. You do not need an official X developer account. You do not need to connect or use an X account for supported scr…

My AI Stand. Realtime by day, rewriting itself by night. Summon my AI superpower.

Open-source coding agent for your terminal, built in Rust and on a journey of continuous community improvement. Issues and PRs welcome.

观澜 / Guanlan：AI Agent 的中文互联网研究、阅读与信源路由工具。

Mac Agent for macOS 26: the agentic AI harness for your Mac Desktop. Computer use, automation, scripting, coding, and more. Powered by 18+ providers across loca…

Semantic version control => entity-level diffs, blame, and impact analysis on top of git. 28 languages via tree-sitter. Built for coding agents.