LLM Mart Basic

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

Run RNA velocity analysis with scVelo on single-cell RNA-seq data — estimate cell-state transitions from spliced/unspliced mRNA dynamics, infer trajectory direction, compute latent time, and identify driver genes. Use when adding directionality to trajectories or studying differe

Train deep generative models for single-cell omics with scvi-tools — probabilistic batch correction and integration (scVI), reference-mapping transfer learning (scArches), differential expression with uncertainty, and multimodal models (totalVI for CITE-seq, MultiVI for multiome)

Analyzes spatial transcriptomics with squidpy (1.8.x) on AnnData and SpatialData objects, routing platforms correctly: Visium spots use spatial_neighbors(coord_type='grid') and pair with deconvolution, while Xenium/MERFISH single-cell data use coord_type='generic'/Delaunay neighb

Store and query genomic variant data at scale with TileDB-VCF — ingest VCF/BCF into compressed TileDB arrays, add samples incrementally, run fast parallel region/sample queries, and export back to VCF. Use when managing population-genomics variant datasets that are too large for

Wraps RDKit in a high-level, pandas-friendly datamol interface with sensible defaults for everyday drug discovery — SMILES/SDF loading into DataFrames, molecule standardization, descriptors, fingerprints, Butina clustering, 3D conformer generation, scaffold analysis, and parallel

Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet benchmark datasets, and pre-trained models (ChemBERTa, GROVER) for property prediction (ADMET, toxicity, solubility) via traditional ML or graph neural networks. Use when running end-to-end

Predicts protein-ligand binding poses with DiffDock diffusion-based molecular docking from PDB structures and SMILES, producing pose confidence scores for virtual screening and structure-based drug design. Use when docking ligands into a protein, generating binding poses, or scre

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

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.

Setup CI/CD pipeline with automated security checks for Solana programs

Configure MCP server API keys in .env

Run tests and automatically fix common issues

Run .NET/C# tests for Unity projects and backend services

Run Rust tests for Solana programs and backend services

Run TypeScript tests for Solana frontends and Anchor programs

Update solana-ai-kit to latest version from upstream

Generate documentation for Solana programs, APIs, and components

Seventy-two slash commands for Claude Code, grouped by what you are doing.

Find missing aliases

Move cold material out of the wiki

Ask a question answered only from the vault

Audit what an agent did

Bulk import an archive in batches

Find the pages holding the graph together

What I have revised

Build or update your CLAUDE.md

Show what the vault is actually about

Commit the current state with a useful message

List open commitments

Open‑WebUI Tools is a modular toolkit designed to extend and enrich your Open WebUI instance, turning it into a powerful AI workstation. With a suite of over 15…

The token-efficient agentic coding workbench. Built for a future where every token counts — it optimizes token usage at the agent-loop level, saving 70%+ on lon…

MCP server for controlling a real iPhone via macOS iPhone Mirroring...and any MacOs app. Screenshot, tap, swipe, type — from any MCP client.

One desktop for all your AI coding Agent — Claude Code, Codex CLI & Gemini CLI. Auto-detect, one-click install, unified chat, file explorer, terminal & editor.…

Pi — A cross-platform AI coding agent, bringing the Claude Code experience to your desktop. No environment setup, no terminal commands. Download and start codin…

DeepSeek Harness Desktop (dsh-desktop). EAC: Embracing All Creation (揽尽万象). Bundled Node.js runtime with full dsh-CLI kernel, one-click startup, 10 built-in UI…

A telegram bot for searching and auto-saving.

金蝶云星空 K3Cloud MCP Server，让 AI 助手（Claude Desktop、Claude Code、Cursor、Cline、Cherry Studio、Openclaw 等任意支持 MCP 协议的客户端）通过自然语言查询和操作金蝶 ERP 系统。

Rewrite frontier research using allegorical structural mapping.

Free4Chat is a temporary collaboration fabric for Humans and Agents.

Give any AI agent a full desktop — it sees the screen, clicks, types, and runs apps like a human. Automate anything with a UI: browsers, legacy software, intern…

A personal AI agent that can work safely on your machine, remember useful context, and keep its data under your control.

A framework for AI-driven economic activity. Declarative, composable, observable, deterministic.

Open-source, self-hosted customer support desk in a single binary. A lightweight alternative to Intercom, Zendesk, Chatwoot.

54 rigorous skills for Codex, OpenCode, and Pi: code review, security audit, feature development, frontend design, MCP tools, Hugging Face ML/training, and more…

A wonderful list of Game Development resources.

Open Science Desktop — local-first, model-agnostic AI research workbench for macOS, Windows & Linux. Open-source Claude Science desktop alternative built on Tau…

Lexora — Personal AI workspace built around Desktop / 以 Desktop 为核心的个人 AI 工作台

Open-source, AI-native Evernote alternative with native MCP. Zero-cost on Cloudflare or self-hosted with Docker.

Full job-hunt Claude skill bundle — Job Description decoder + Resume builder (11 templates) + Behavioral Interview / story bank. Three self-contained sub-skills…