LLM Mart Basic

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running populat

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when p

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phen

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/p

Run ESM protein language models — ESMC for embeddings and representations, ESMFold2 for structure prediction, and ESM3 for generative multimodal protein design across sequence, structure, and function — locally or through the hosted Biohub Platform API (formerly Forge). Use when

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting t

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting chan

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preproces

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or

Analyze Neuropixels 1.0/2.0 extracellular electrophysiology with SpikeInterface — load SpikeGLX/Open Ephys recordings, preprocess and motion-correct, run Kilosort4 spike sorting, compute quality metrics, apply Allen/IBL curation, and do AI-assisted visual inspection. Use when wor

Runs FASTQ-to-VCF germline and somatic variant calling via the Nextflow nf-core/sarek pipeline pinned to -r 3.10.0 — builds the samplesheet.csv (patient, sex, status, sample, lane, fastq_1, fastq_2), runs bwa-mem/bwa-mem2/dragmap alignment plus GATK4 MarkDuplicates and BQSR again

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 datase

Build phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstruct

Design protein sequences for a fixed backbone with ProteinMPNN (Dauparas 2022) — message-passing inverse folding that outputs sequences predicted to fold to a given structure, with fixed positions, tied/symmetric chains, amino-acid bias, and a soluble-model variant. Use when inve

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

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.

Treat an AI agent skill as both an instruction package and a software dependency: inspect what it says, what it runs, what it can access, and how it updates.

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

Compare two things from your own sources

Find the path between two ideas

List unresolved contradictions

Argue against me

List decisions made

Find near-duplicate pages

Check the setup is working

Draft from the vault

Preview a run without writing

Explain it back and find the gaps

Export a page or set of pages

What is missing from my understanding

Export the graph for outside analysis

Report the shape of the graph

Prepare a handoff brief

Claude Code skills for Chinese-narration recaps from supported video files, with optional editable JianYing/CapCut draft export. | 用 Claude Code skills 为支持的视频文件…

Drive the Unity Editor from an AI agent or the terminal. The Editor serves MCP itself over HTTP, so there is no second process to run, and the isuzu-unity-cli c…

面向企业的数字员工构建与运行平台：把专业员工的经验、流程与判断标准，固化为可随时上岗、可配置、可审批、可观测的 AI 数字员工。

A local-first, Pi-powered AI agent workspace for Desktop, WebUI, and CLI

660+ muapi-hosted generative-media models plus community-submitted third-party API tools (SEO, enrichment, social, scraping) — one YAML file per entry, browsabl…

A compounding agent OS for recursive agents. Also an open source alternative to Grok Bot and Meta's Muse.

Independent desktop client for OpenCode 2. Manage projects, sessions, parallel agents, requests, and changes on Linux and macOS.

Production agent skills for Claude Code, Cursor, and any SKILL.md harness — Codex fleets, video pipeline, monorepo review bundles, multi-chain explorer.

See and manage what your coding assistants load — skills, commands, subagents, plugins and MCP servers, with real usage.

An Enterprise-Grade Full-Stack RBAC Permission Management System Built with Go + React

Create AI Agents in a No-Code Visual Builder or TypeScript SDK with full 2-way sync. For shipping AI assistants and multi-agent AI workflows.

基于 DeepSeek Harness（DSH）的稳定桌面端，集成Git、内置浏览器与记忆功能 | DeepSeek Harness desktop GUI with local workspaces, Git, browser and memory.

⚡ Control Apache Airflow with natural language via MCP. Chat with your workflows using Claude, GPT, or any LLM — no REST API calls needed. Supports Airflow 2.x…

Open-source CLI, schemas, resolver, and DSH agent tools for DSH Plugin Hub

Pi Coding Agent 中文学习蓝皮书：从安装与第一个可验收任务开始，逐步掌握 Session、Context、Skill、Extension、Subagent 与长期 Agent 工作流。

Self-hosted framework for orchestrating fleets of specialist AI agents — ensemble reasoning and a full agentic coding pipeline, model-agnostic and local-friendl…

Self-hosted, vendor-neutral control plane for your local coding agents (Claude Code & Codex). Run your agents, on any plane.

A practical AI agents handbook covering agent systems, agentic workflows, LangGraph, MCP/A2A, context engineering, agent memory, evaluation, observability, and…

Vibe Coding 从入门到精通教程｜AI 结对编程工作流｜Prompt、Skill、Workflow、上下文管理、codex实战指南

Static security scanner for LLM agents — prompt injection, MCP config auditing, taint analysis. 51 rules mapped to OWASP Agentic Top 10 (2026). Works with LangC…