LLM Mart Basic

Computes mass-spectral similarity and identifies compounds for metabolomics with matchms — comparing mass spectra, scoring similarity (cosine, modified cosine), and searching spectral libraries to annotate unknowns. Use when matching MS/MS spectra, identifying metabolites, or lib

Applies medicinal-chemistry filters with the medchem library — drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, and molecular complexity metrics for compound prioritization and library cleanup. Use when filtering or triaging a compound library, flagging PA

Featurizes molecules for machine learning with molfeat — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, pharmacophore and shape descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, CheMeleon) exposed as scikit-learn transformers that convert S

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark datas

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization,

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), wi

Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning. Use when a project specifically needs TorchDrug's dat

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence

Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a doc

Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when

Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, wo

Develops, tests, and validates clinical machine learning models with the PyHealth 2.x healthcare AI toolkit. Use when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, length of stay, drug recommendation), medical coding systems (ICD

Generates concise (3-4 page), focused medical treatment plans in LaTeX/PDF format across all clinical specialties — general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management — using SMART goal framew

Verifies that every bibliography entry actually exists by cross-checking Crossref, OpenAlex, Semantic Scholar, and arXiv (no API key required) plus doi.org DOI registration, fuzzy-matching title and authors (difflib ratio >= 0.70), flagging retractions recorded by Crossref (inclu

Runs a 13-agent deep research pipeline for rigorous academic work on any topic across 7 modes (full research, quick brief, paper review, lit-review, fact-check, Socratic guided research dialogue, and systematic review with optional meta-analysis), covering research-question formu

Audits and repairs Markdown link health across a skills repo via a four-tier pipeline (config hardening, intra-repo file-ref fixes, external URL substitutions, residual exclusions) and enforces a Tier 3 substitution guardrail that prevents regressions of previously-passing links;

Drafts and revises academic papers through a 12-agent pipeline with hardened LaTeX output (apa7 class, PDF compiled from LaTeX), supporting IMRaD, literature review, theoretical, case study, policy brief, and conference paper structures, APA 7.0 (default), Chicago, MLA, IEEE, and

Orchestrates the full academic research pipeline (research, write, integrity check, review, revise, re-review, re-revise, final integrity check, finalize), coordinating alterlab-deep-research, alterlab-paper-writer, and alterlab-paper-reviewer into a seamless 10-stage workflow wi

The AlterLab front door and multi-agent launcher — routes a task to the right AlterLab skill(s) when the user invokes the suite without naming one, and for a multi-stage goal (or on the keyword 'alterflow', aliases 'alterresearch' / 'ultralab') it clarifies the goal with a few qu

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.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

Author a numbered, dated, user-attributed Architecture Decision Record under .codearbiter/decisions/.

Assemble the governance record for a range — commits, overrides, ADRs, sprint auto-decisions, open questions, checkpoint findings — into one dated audit packet. Read-only.

Lightweight Q&A about the project — answer from context and return, no routing, no state change.

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

Finish an already-merged branch — classify the leftover artifacts, return to a fast-forwarded default checkout, and delete the merged local branch. Every discard confirmed per item; containment proven, never assumed.

Show the codeArbiter command catalog — the public command list and what each routes to.

Run the full commit gate — the only sanctioned path to a git commit.

Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

Optional manual drift audit — report stale provenance-tracked docs, then per stale doc offer re-scout, re-baseline, or defer. Not the daily loop; commit-gate auto-heal owns routine maintenance.

Brownfield back-fill — scout an existing codebase and populate .codearbiter/, then lock it initialized.

Investigate-then-decide root-cause analysis for a defect whose cause is unknown. No code changes — exits to /ca:fix, /ca:adr, or a no-action close.

Greenfield decomposition interview — a layered interview that populates .codearbiter/ and locks it initialized.

Verify the active host install, package, command ownership, enforcement, and harmless live-fire probe. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Author a new codeArbiter skill: prove the gap is real, get the spec approved, then write it.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

Implementation of Podlite markup language

Open-source AI video workbench. Bring any model or your local ComfyUI, and let Claude Code / Codex / Cursor direct it over MCP — storyboard, references, generat…

《深入理解 AI Agent：设计原理与工程实践》（李博杰 著）开源主仓库：全书正文、编译版 PDF 与按章配套代码

Distilly — Distill how they think into reusable Skills for any Agent or Bot. Formerly Colleague Skill（原同事 Skill）.

本地优先的类飞书 Markdown 编辑器,内置可审改的 AI 助手 | Local-first WYSIWYG Markdown editor with a reviewable AI agent

A lightweight all-in-one terminal with 20+ protocols — SSH, RDP, SFTP, databases, Kubernetes and more. With a built-in autonomous AI Agent that plans and runs m…

一款专注于桌宠方向的AIAgent。特点是一键安装、功能齐全、极低开销、完全暴露上下文、全功能插件化、AI自主插件开发、永久唯一会话、类游戏引擎交互策略。具有极高的扩展性和拟人程度上限，非常适合想长期培养和自定义需求高的用户。

Control Gmail, Google Calendar, Docs, Sheets, Slides, Chat, Forms, Tasks, Search & Drive with AI - Comprehensive Google Workspace MCP Server & CLI Tool

一个先接住情绪、再分析关系并给出可执行策略的 Codex 恋爱军师，内置心理、法律、社会、人文、哲学、婚姻家庭与性学知识库，支持多元关系。

AI-powered SRE platform — read-only infrastructure diagnostics with deep investigation, security governance, and team collaboration

An open-source AI desktop companion inspired by Cyrene, combining immersive Chat, personalized long-term memory, and an agentic Work mode.

A local-first AI agent with persistent memory, emotional intelligence, and a peer-to-peer skills economy.

The open-source, multi-agent alternative to Claude Tag. @ any agent, wherever work happens, your agents work alongside your team and each other, learning as the…

Simple LLM service identification - translate IP:Port to Ollama, vLLM, LiteLLM, or 60+ other AI services in seconds

🔥 Official Firecrawl MCP Server - Adds powerful web scraping and search to Cursor, Claude and any other LLM clients.

Claude in Chrome, reverse-engineered and open-source. No domain blocklist. Any Chromium browser. Same 18 MCP tools, same performance.

Agent-native flight & hotel search and booking — MCP server, CLI, and Python/JS SDKs. Hundreds of airlines plus the major booking sites, with per-flight reliabi…

Open-source desktop AI agent for tools, files, knowledge, workflows, and real deliverables.

Open-source AI job search: scan job portals, evaluate listings into a structured A-H report with a global 1-5 score, tailor your CV, track applications — runs l…

Privacy-first Codex skill for discovering, validating, completing, and tracking job applications