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.

Iniciar planificación de archivos estilo Manus. Crear task_plan.md, findings.md, progress.md para tareas complejas.

Bridge Claude Code's /goal to the active plan. Derives a goal condition from task_plan.md and invokes /goal so Claude keeps working until the plan is complete. Available since v2.38.0.

Run a planning-aware cadence with Claude Code's /loop. Default tick checks plan status, runs check-complete, nudges progress.md update if stalled. Available since v2.38.0.

启动 Manus 风格的文件规划。为复杂任务创建 task_plan.md、findings.md、progress.md。

啟動 Manus 風格的檔案規劃。為複雜任務建立 task_plan.md、findings.md、progress.md。

Start Manus-style file-based planning. Creates task_plan.md, findings.md, progress.md for complex tasks.

Short alias for /plan. Starts Manus-style file-based planning: task_plan.md, findings.md, progress.md. Available since v3.0.0.

Implements Manus-style file-based planning for complex tasks. Creates task_plan.md, findings.md, and progress.md. Use when starting complex multi-step tasks, research projects, or any task requiring >5 tool calls. Now with automatic session recovery after /clear

Show current planning status at a glance - phases, progress, and any logged errors.

Run three-agent adversarial analysis -- advocate builds the case, adversary challenges it, judicial analyst synthesizes

Structured pre-execution briefing session -- collects case context through specialist panel, builds execution plan, supports resume and depth control

Analyze cantonal law for all 26 Swiss cantons -- cantonal court decisions, cantonal legislation, procedural specifics, and interaction with federal law

Validate, format, and look up Swiss legal citations including BGE/ATF/DTF decisions and statutory references

Create a reusable custom workflow by combining BetterCallClaude agents. Interview-based: pick agents, order them, define the output. Saved for future use with /bettercallclaude:workflow.

Analyze Swiss legal documents -- identify legal issues, extract key clauses, verify citations, and assess compliance

Diagnose MCP server connectivity — tests each server, reports status and impact in plain language, suggests fixes for issues.

Draft Swiss legal documents including contracts (OR), court submissions (ZPO), and legal opinions (Gutachten) with multi-lingual support

Force Federal Law Mode for Swiss federal legal analysis, overriding cantonal auto-detection

Show complete BetterCallClaude command reference, available agents, skills, and usage examples

Execute the BetterCallClaude 5-step Swiss legal framework: intake → research → strategy → adversarial → draft. A complete end-to-end pipeline for any Swiss legal matter, from document analysis through final legal output.

AI agent orchestration kit for Windows, Linux/MacOS with Codex skills, hooks, routing rules and profiles for Claude, OpenCode, Cursor, Gemini and Windsurf.

Skills & reviewer agents for AI-first climate science — built and used by a PhD atmospheric scientist

出行路书工作流 skill：联网实查 + 多源交叉验证，产出可核验、能执行的旅行攻略。覆盖吃住行游拍避全维度，附美食情报卡、基准骨架与校验工具，支持一键部署在线版。

Self-hosted AI code reviewer with indexed PR reviews, walkthroughs, vulnerability scanning, dependency graphs, custom rules, and a learning loop.

🧬 Extend EvoScientist with Installable Skill & Knowledge Packs

Give the agent a machine. Just not yours. Each AI coding agent gets its own isolated machine with root, Docker, and systemd - active defense detects and stops t…

Automatic memory consolidation for OpenClaw agents — like sleep for your AI. Powered by MyClaw.ai

🗂 The essential checklist for modern web development, for humans and AI agents

Distribb CLI, Claude, Codex, Hermes, OpenClaw skill for AI-powered SEO. Write content with your own AI, publish through Distribb's backlink network.

Open-source AI browser agent — type plain-language commands and Bah operates the web for you. Works with cloud AI (DeepSeek, Mistral, NVIDIA) or local Ollama mo…

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…

Use your ChatGPT / Codex subscription with DeepSeek Harness via OAuth, with model access, usage quotas, search, and image generation — no API key or Codex CLI r…

Local-first A-share research workbench for DeepSeek Harness: market dashboards, watchlists, valuation, four investor agents, versioned reports, and continuous p…

Open-source video pipeline (clipper, AI video & more) — scout trends, clip long videos, generate captioned shorts, design motion graphics. Local-first, BYOK. AG…

Desktop app for the pi coding agent: streaming timeline, Git review with hunk staging, session tree, native UI for pi extensions. Windows · macOS · Linux. pi 编程…

Zero-dependency browser video editor that AI agents can drive — JSON timeline, MCP + REST, live-reloading UI

Personal Context Manager for Claude Code. Your life in walnuts.

Fast way to switch between Claude Code configuration profiles

AutoClip｜一个链接，一键出片。开源 AI 视频剪辑桌面工具，将播客、访谈、课程等长视频自动剪成短视频，生成字幕、封面和发布文案，适配抖音、小红书、TikTok、Reels 与 YouTube Shorts。Open-source AI video clipping & content repurposing.