LLM Mart Basic

Loads, runs, and fine-tunes pretrained models with Hugging Face Transformers v5 (PyTorch-only) — pipeline() inference for chat-model text generation, text classification, NER, zero-shot, speech recognition, image classification, object detection, and image-text-to-text VLMs; Auto

Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessing (e.g., HDBSCAN), and supervised or parametric UMAP. Use when projecting high-dimensional data to low dimensions for visualization, embedding generation, or as a

Out-of-core tabular analytics with Vaex — memory-mapped HDF5/Arrow/Parquet via vaex.open, lazy virtual columns, delayed single-pass aggregations on billion-row tables, binned histograms/heatmaps, and vaex.ml transformers on one machine. Vaex is in minimal-maintenance mode (vaex-c

Access the AlphaFold DB of 240M+ AI-PREDICTED protein structures (v6, plus precomputed homodimer/heterodimer complexes) — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computat

Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical enginee

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a p

Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the A

Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or substrate specificity for

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how o

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a targe

Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or expor

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assess

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or inte

Use when conducting security assessments — OWASP Top 10 / API / LLM, CWE Top 25, CVSS scoring — auditing PHP/TYPO3, APIs, frontend, Terraform/K8s/Docker IaC, AWS cloud, AI agent configs, or scanning dependencies.

Look up and apply Python builtin and standard-library time and space complexity when analyzing code, reviewing performance, or comparing operations. Includes implementation and version qualifications. Use for complexity analysis, not general Python syntax questions.

Designs and reviews tests for every complexity, behavioral, and performance claim in documentation. Use when adding or changing claims, auditing claim or API coverage, or creating module complexity tests.

Updates this repository's supported Python range when an old version reaches EOL or a new final version is released. Covers package metadata, CI pins, version references, documentation, translations, public API manifests, tests, and lockfile verification.

Run a user-authored playbook from the vault: a multi-step guided procedure. Lists available global and local playbooks, selects one by trigger, and drives its steps in order — spawning per-step sub-agents or running inline, pausing at review gates.

Cut a booping plugin release — verify the version bump against the last published tag, draft public-voiced release notes, merge the release branch into master, tag, and publish the GitHub release. Use when cutting a vX.Y.Z release of this repo.

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.

Ingest your own finished work

Ingest newsletters without duplicating

Ingest an academic paper

Ingest a PDF

Clip and ingest a web page

Ingest a voice note

Ingest a video or podcast transcript

Ingest new material from raw/ into the wiki

Scaffold a new vault

Install the skills, commands and agents

What do I know about a topic

Find and add missing connections

Audit structure and repair what is mechanical

Merge two pages

Record a dated metrics snapshot

The monthly structural review

Find unreachable pages

Outline a piece from your concept pages

Audit what should not be in the vault

Where a project stands

Build AI Agents like playing LEGOs. Everything is a Plugin.

The coding agent that answers to you, your model, your machine, your rules.

CI-native agent CLI tool for deterministic pipeline gating.

Local-first cross-platform desktop workspace for Claude Code / agents: multi-agent, Git worktrees, code diffs, skill marketplace, multi-model, Computer Use, tas…

Local-first visual generation runtime and studio for people and coding agents, with reproducible image and video workflows across multiple providers.

A token-efficient MCP server for safe, line-oriented text file editing with partial reads, hash-based conflict detection, and atomic multi-file operations.

Open-source, evidence-driven MCP server for RTL simulation debugging: correlate VCS/Xcelium logs, VCD/FSDB waveforms, SystemVerilog/UVM source, hierarchy, and c…

runs anywhere. uses anything

One macOS app for Claude Code, Codex, and every agent runtime you use — scheduled runs, global hotkey launcher, per-run git worktrees, one review board.

Soul-driven AI agent with permission-hardened tools, token budgets, and multi-channel access. Runs 24/7 from CLI or Telegram.

Email, SMS & phone-call infrastructure for AI agents — send and receive real email and text messages, and place agent-driven outbound voice calls, all programma…

55 MCP tools to drive the Unity Editor from any MCP-compatible AI agent — scenes, GameObjects, prefabs, assets, tests, and builds. OpenClaw gateway included for…

Google Ads MCP + Meta Ads MCP + GA4 in one server for Claude, ChatGPT, Cursor & n8n — 250+ tools, hosted remote MCP, OAuth login, no API keys. By Ryze AI.

Claude Code & Codex 本地 token 追踪 — 状态栏（Codex 业界首创伪 statusline）、GitHub 风格热力图、多模型成本分析。 | Local token tracker for Claude Code & Codex — status line (industry-first…

Empower the Shell to think. Evolve Operations.

🤖 A full-stack Agent Chat Runtime for pre-production validation, built with act, TypeScript, and LangGraph JS combining streaming, multimodal, HITL, and tools…

Cerul — video memory infrastructure for AI products. SDKs, CLI, MCP, and developer integrations.

Stealth headless browser for AI agents — bypass Cloudflare, bot detection, and anti-scraping. Drop-in Puppeteer/Playwright replacement.

Web research for your agents with smart and safe tooling + knowledge store

FuXi is a fast, self-contained AI coding agent that lives in your terminal — edit code, run commands, and drive tools, with cost-aware routing across LLM provid…