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.

Find concept pages nobody has touched

Audit the tag vocabulary

How my sources developed over time

Show which pages an answer used

Add relation types where they matter

The weekly review

Implement an approved plan or issue in its own worktree, run the gate, open the pull request.

Close a finished session: sweep for unfinished work, land and hand off, file the follow-ups, tell the sessions that depend on this one, then archive.

Write the repository handoff file for the next session, and record any durable learning.

Merge an approved pull request, clean up its worktree and branch, then check whether a release is due.

Turn a topic or issue into a plan the reviewer approves in the native plan pane.

Answer a research question with parallel read-only gatherers and one synthesized digest.

Review the branch's diff in two fresh contexts — scope against the spec, then quality — and report findings only.

Transform a vague prompt into precise, structured AI instructions

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