LLM Mart Basic

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

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

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.

Log derived files and trace provenance back to ENCODE source data

Store, check, or clear ENCODE API credentials for restricted data

Assess ENCODE experiment quality using audit counts and replicate counts

Search ENCODE experiments by assay, organ, biosample, or target

Track ENCODE experiments locally with publications and provenance

List, search, and inspect ENCODE files by format, type, and assembly

Generate ENCODE citations for publications, grants, and presentations

Check if two ENCODE experiments are compatible for combined analysis

Cross-reference ENCODE data with PubMed, GEO, ClinicalTrials, and bioRxiv

Download ENCODE files (BED, FASTQ, BAM, bigWig) with MD5 verification

Log derived files and trace provenance back to ENCODE source data

Store, check, or clear ENCODE API credentials for restricted data

Assess ENCODE experiment quality using audit counts and replicate counts

Search ENCODE experiments by assay, organ, biosample, or target

Track ENCODE experiments locally with publications and provenance

Record the present state by mode — decision (ADR, RFC, rule), code (spec, doc, guide, scenario), or research (a ready report or one external material); a gate picks the document type.

First-time Archcore setup — wire host configs, measure the authored context, compose the full first-day seed in one preview, and create it on one confirm; import converts CLAUDE.md, AGENTS.md, rule files, ADRs, and docs into native documents; refresh adds new facts or drills into one domain.

Plan a feature or initiative through a computed route — a small fix exits with no documents, one capability gets a spec and a plan, a large initiative gets an umbrella PRD with one spec per capability; start with sdd, sources (market research), iso (regulated work), or research (technical investigation) to run that path directly.

Review branch changes against Archcore docs, or report project health; drift runs staleness detection, deep a full documentation audit, closeout closes a finished feature, experience captures a repeated pattern.

Verify that citations actually exist and that the claims they support are faithful to the cited source. Runs deterministic existence checks (Crossref / OpenAlex / Semantic Scholar / arXiv) plus a claim-faithfulness pass via the alterlab-citation-verifier skill.

面向中文开发者的 Claude Code Skills / Agents / Plugins 精选与原创技能库｜按场景分类｜复制即装｜持续更新

原生 macOS Git 客户端，以 Agent 驱动仓库管理、审阅与协作。

A 股短线复盘看板：涨停池·连板梯队·龙虎榜·板块资金一屏看完，赚钱效应/晋级率/梯队断层/情绪周期等派生指标纯计算直出（不经过 AI），AI 只把数据串成能读的盘面研判。全本地运行，可用 Claude/Codex 订阅免 API key。| A-share short-term daily-review dashbo…

禁漫天堂 Agent Skills / AI 原生 JMComic 助手：通过 MCP 与 Skills 将 JMComic 注入你的 AI Agent. / AI-powered JMComic assistant for seamless integration with AI Agents via MCP & S…

Pairlet (formerly CC Pocket / cc-pocket) — Continue your local AI coding tasks from phone, tablet, or desktop.

Self-hosted Personal AI + agent runtime in .NET (NativeAOT-friendly)

A self-hosted knowledge platform for humans and AI agents — publish wikis, blogs, and portable Agent Skills.

Notion CLI with AI agent support. Smart queries, Obsidian sync, batch ops, backups, validation and more.

AI Coding Agent Multiplexer

Independent executor–verifier orchestration for software changes.

AI-native, local-first video editor by Ribbi — runs entirely in the browser. Rust/WASM engine, WebGPU compositing, WebCodecs export; humans and LLM agents edit…

Distill your knowledge, memories, and decisions into an open-source, inspectable AI Agent Twin.

🔬 Harness Vibe Research with Self-evolving AI Scientists

Personal AI desktop agent for Windows, macOS, Linux, Android & iOS. Set a goal, it works on its own. Teams (pair two desktops, agents + humans), Agent2Agent, Wo…

Run agents like a company. AgentOS is the native control plane for OpenClaw — manage agents, tasks, models, context, approvals, and runtime visibility from one…

Create Agentic admin panels faster on TypeScript and Vue.js with AdminForth Framework. Setup main CRUD pages within minutes, extend as you need

OpenJudge: A Unified Framework for Holistic Evaluation and Quality Rewards

An ebook reader with a self-evolving agent: it remembers your reading across books, and plugins extend the reader and the agent alike.

A curated list of awesome resources for vibe coding

Agentic Voice Notes for iPhone and macOS - Rust, Dioxus, LanceDB + RIG + SQLite