LLM Mart Basic

Generate publication-ready methods sections, figure legends, supplementary tables, and data availability statements from ENCODE analysis provenance. Implements the scientific documentation standards requiring complete metadata reporting. Use when the user needs to write methods,

Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq dat

Search and explore ENCODE Project genomics data. Use when the user wants to find experiments, files, or explore what data is available for specific assays, organs, cell lines, or targets.

Set up the ENCODE Toolkit server connection. Use when the user needs help installing, configuring, or troubleshooting the ENCODE connector.

Find and work with ENCODE single-cell genomics data including scRNA-seq and scATAC-seq. Use when the user asks about single-cell experiments, cell type resolution, clustering from ENCODE data, deconvolution of bulk signals using single-cell references, or comparing single-cell vs

Track ENCODE experiments locally with publications, citations, and provenance. Use when the user wants to build a collection of experiments, manage citations, compare experiments, or track data provenance.

Query the UCSC Genome Browser REST API to retrieve regulatory tracks, DNA sequences, cCRE annotations, TF binding clusters, and track schemas for any genomic region. Use when the user wants to look up what regulatory elements exist at a genomic locus, retrieve DNA sequence under

Annotate genetic variants (GWAS hits, eQTLs, rare variants) with ENCODE functional data to interpret non-coding variation. Use when the user has variants of interest and wants to understand their regulatory context, identify causal variants from GWAS loci, assess variant impact o

Comprehensive guide for visualizing ENCODE data including deeptools heatmaps, IGV screenshots, UCSC track hubs, and publication-quality plots. Use when users need to create visualizations of ChIP-seq signal, peak landscapes, genome browser views, or any visual representation of E

Make software health, failure, degradation, and recovery visible through useful observability and diagnostics. Use when adding logs, metrics, traces, health checks, alerts, incident signals, or operational feedback.

Inspect the real repository, environment, dependencies, and runtime evidence before designing or changing software. Use for greenfield construction, unfamiliar codebases, uncertain behavior, or any task where assumptions could create rework.

Reflect on failures, incidents, reviews, and completed software work to turn evidence into durable tests, guardrails, documentation, and process improvements.

Debug software by making failures visible, reproducing them, finding contributing causes, and adding durable regression protection. Use for bugs, failing tests, incidents, regressions, flaky behavior, and unexplained production errors.

Improve software continuously through small, safe, behavior-preserving changes that reduce maintenance cost. Use for refactoring, cleanup, technical debt, naming, duplication, dead code, or post-change polish.

Choose simple, maintainable software designs by removing speculative complexity, comparing alternatives, and making explicit tradeoffs. Use for architecture, API, data-model, dependency, and scope decisions.

Implement software through small, repeatable, integrated vertical slices with clear exit criteria and honest verification. Use when a design is understood and code needs to be built or changed.

Review software with careful attention to correctness, maintainability, security, operations, and meaningful detail. Use for diffs, branches, pull requests, architecture decisions, or final quality checks.

Author a greenfield build blueprint in four gated stages — business logic, tech stack, logic-to-stack mapping, and a phase plan — each requiring explicit user approval before the next. Use when building a new project or a substantial new subsystem from scratch.

Step 0 of consequential software work under Monozukuri. Classify the task, assess its risk tier, choose execute or sensei mode, and compose the sequence of Monozukuri skills and the Definition of Done for it. Skip for trivial one-line edits, pure questions, and throwaway scripts.

Clarify software goals, constraints, stakeholders, and risks before consequential design or implementation work. Use for greenfield ideas, ambiguous requirements, architecture decisions, or changes where misunderstanding would be costly.

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.

Analyze code performance and propose three specific optimization improvements

Configure and initialize a project following the Product as Code specification for structured, version-controlled product management

Create a new epic following the Product as Code specification with guided workflow

Create a new ticket within an epic following the Product as Code specification

Update ticket status and track progress in Product as Code workflow

Validate Product as Code project structure and files for specification compliance

Audit application performance metrics

Conduct comprehensive PR review from multiple perspectives (PM, Developer, QA, Security)

Prepare and validate release packages

Load project context by reading key documentation files and exploring project structure

Analyze overall project health and metrics

Simulate project outcomes with variable modeling, risk assessment, and resource optimization scenarios.

Sync project structure to Linear workspace

Intelligently refactor and improve code quality

Prepare a new release by updating changelog, version, and documentation

Safely remove a task from the orchestration system, updating all references and dependencies.

Generate comprehensive reports on task execution, progress, and metrics.

Reproduce a specific issue by creating a failing test case

Resume work on existing task orchestrations after session loss or context switch.

Analyze team retrospectives for insights

PiG (Pi in Go) is a faithful Go port of upstream Pi, the TypeScript codebase behind the Pi coding agent. It is a parity-bound translation, not a rewrite: upstre…

An AI Agent that lives in your pocket. Local-first and privacy focused.

Unofficial skill that teaches coding agents to build with TypeSafe AI's Jev: typed decisions, calibrated confidence, and prior art from 150+ community projects.

Adaptive Test-time Learning and Autonomous Specialization

Prediction-market trading engine — Wang Transform pricing on 291K+ contracts; paper-traded across Kalshi · Polymarket · Solana DFlow (Jito bundles) · 633 tests

Knowledge Management for Humans and Agents

Open-source Claude Cowork / Codex / WorkBuddy alternative — a local-first AI office agent that turns one request into real PPTX, DOCX, XLSX and HTML files. Runs…

DeepAgent Code: AI coding agent with persistent memory and control plane

Awesome Jev — evidence-graded index of TypeSafe System One: SDKs, MCP tools, agents, apps and open models. 20 languages, rebuilt every 2 hours.

CLI for Telegram — agent-friendly, daemon-based, with webhook event push.

AI deep-research agent that turns any question into a cited report: plans searches, reads real sources, verifies evidence. Self-hosted, multi-provider, Docker-r…

Event-stream AI Agent framework for building your persona bot 🍊

Give the agent a machine. Just not yours. Each AI coding agent gets its own isolated machine with root, Docker, and systemd - active defense detects and stops t…

Local Emperor-style AI agent with Vue WebUI, multi-provider LLMs, streaming chat, tools, skills, memory, and token telemetry.

Open-source AI reverse-engineering agent platform and MCP server for Ghidra, Frida, x64dbg and Rizin — automated PE/APK/binary analysis, CTF and malware researc…

"Never send a human to do a machine's job" - Open Source AI hacking agent

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