LLM Mart Basic

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

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

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.

Add remote HTTP or local stdio MCP servers to Claude Code, choose the right scope, protect credentials, verify the connection, and test with least privilege.

Skills teach Claude a repeatable method, connectors provide governed access to apps and live data, and plugins package related capabilities for installation and sharing.

Use an agent skill to package reusable know-how and workflow instructions. Use an MCP server when an agent needs live, governed access to external data or actions.

Custom commands and skills can both create a slash-invoked workflow in Claude Code. The important choice is how the workflow is discovered, shared, and permissioned.

A useful Claude skill solves one recurring engineering job, is easy to inspect, and saves more time than it creates in setup and review.

Claude skills can live in your Claude account, your local Claude Code setup, or a repository. Install them where the sessions that need them can load them.

Build a portable AI agent skill from one repeatable job: a precise description, concise instructions, focused resources, and tests that prove it works.

AI agent skills package instructions, scripts, references, and templates into portable folders an agent loads only when the task calls for them.

AI made publishing cheap, which is exactly the problem. What separates a page worth ranking from a competent summary of the first ten results.

A prompt that works once isn't a quality system. Five cases, an observable rubric, and a regression set will tell you whether a change helped.

One character of YAML, four pods that never started, and two safety nets I didn't know were holding. Every restart is an audit. Schedule them before they schedule you.

"Verify your work" isn't an instruction. It's a mood. Here's the version that's an instruction. Verify with a different mechanism than the one that made the claim.

A prompt that works once may still fail in production. A lightweight eval set gives you repeatable cases, a clear rubric, and a way to see whether a prompt change actually improved the workflow.

The best AI tool is not the one with the longest feature list. It is the one that solves a defined job reliably, fits the workflow, handles data appropriately, and remains useful after the novelty wears off.

Use AI to speed research without losing trust. Learn to find primary sources, verify claims, preserve uncertainty, and keep an auditable source trail.

Better prompts aren't magic wording. They're short briefs that hand the model a task, the context it can't infer, the limits, and a quality bar.

A green PR, a controller reporting success, and not one line of the new code running

credo - Set the session mode to autonomous (work approved GO items unattended, hook-enforced keep-alive ON)

credo - Initialize session with main agent workflow instructions

credo - Set the session mode to passive (user available for clarifications only, no keep-alive)

credo - Set up Claude Code with recommended workflows and plugins

dogma - Find and fix AI-typical patterns in code (reactive cleanup)

dogma - Sync documentation across README files and wiki articles

dogma - Interactively collect and apply CLAUDE rules to the project

dogma - Add ignore patterns to multiple locations at once

dogma - Run project-specific linting and formatting on staged files (non-interactive)

dogma - Create or update DOGMA-PERMISSIONS.md interactively (Git, File, and Workflow permissions)

dogma - Sanitize git history from Claude/AI traces and fix tracking issues

dogma - Intelligently sync Claude instructions from a source to the current project with interactive review

dogma - Check and fix version mismatches across all version files

Install GSD resources into the active Claude config dir (${CLAUDE_CONFIG_DIR:-$HOME/.claude}/get-shit-done/) (required before using other GSD commands)

Remove GSD resources from the active Claude config dir (${CLAUDE_CONFIG_DIR:-$HOME/.claude})

hydra - Remove already merged worktrees and their branches

hydra - Create a new Git worktree for isolated work

hydra - Safely remove a Git worktree

hydra - Show available commands and explain the concept

hydra - List all Git worktrees of the repository

Make any song you can imagine

Leading AI-powered video generation platform that specializes in creating hyper-realistic talking avatars

Hermes Agent is an open-source, self-improving autonomous AI agent developed by Nous Research

Kilo Code is a popular, open-source AI coding agent and "agentic engineering" platform designed to help developers build, refactor, and debug software faster

General-purpose agent in one static Go binary. ReAct loop, ACP server for IDEs, OpenAI-compatible REST API with embedded web UI, Telegram gateway, cron schedule…

Autonomous agent framework with structured memory, safety hooks, and loop management. Built by the agent that runs on it.

TSP自托管、零运维的 A 股「选股 + 监控 + 回测」量化工作台 | 基于 TickFlow 数据源 | LLM能力驱使策略定制+个股分析+复盘 | 自由接入第三方数据源与个性化扩展数据 | 个人开源 ,非TickFlow官方项目

Curated, verified Agent Skills powered by ModelStudio.

Run Claude Code, Codex, Antigravity, Cursor Agent and OpenCode as one runtime — persistent sessions, multi-agent councils, an OpenAI-compatible endpoint, an MCP…

pi had nothing (nothing), so I made something (something) — sorry mariozechner-senpai, I went ahead and lovingly soiled your pure pi for you. opinionated fork o…

A persistent workspace for development work that self-improves and continues beyond one session.

Open-source memory and context for user-aware agents: scoped memory, provenance, retrieval quality, correction, boundaries, evals, and MCP/HTTP access.

📚 A zero-dependency, git-backed micro-lesson library for AI Agents to asynchronously share and search verified debugging experience. Python stdlib only. | http…

Deterministic, local-first memory and guardrails for AI coding agents with no LLM in the hot path.

Deterministic spec-orchestration for local LLMs in the pi coding agent — drives prompts through refine→research→grill→compose→critique, with bundled web/docs/fe…

Native Safari browser automation for AI agents. 97 tools via AppleScript — zero overhead, keeps logins, runs silently in background. Drop-in alternative to Chro…

Agent OS: keep specialist agents in a hub, spin up a temporary orchestrator per task. Local-first, works with any model.

Git for agent memory. Branches, diffs, PRs, and rollback for what your agents know.

Multi-Provider AI Gateway - No personal logs by design. Model autodiscovery, Failover groups, High availability, Android companion app, and more - "Because we h…

Production-grade MCP server for MikroTik RouterOS with secure AI-native network automation.