LLM Mart Basic

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

Featurizes molecules for machine learning with molfeat — ECFP/MACCS/MAP4 fingerprints, RDKit and Mordred physicochemical descriptors, pharmacophore and shape descriptors, and pretrained embeddings (ChemBERTa, ChemGPT, CheMeleon) exposed as scikit-learn transformers that convert S

Queries the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biomedical relationships across genes, drugs, diseases, phenotypes, pathways, and biological processes. Use when exploring drug-disease or gene-disease links, building disease-centric knowledge subgraphs, or

Loads Therapeutics Data Commons (TDC, PyTDC) AI-ready drug-discovery datasets and benchmarks — ADME, toxicity, drug-target interaction (DTI), scaffold splits, and molecular oracles for therapeutic ML and pharmacological prediction. Use when fetching a standardized benchmark datas

Provides the RDKit cheminformatics toolkit for low-level, fine-grained molecular primitives — SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure/SMARTS search, 2D/3D coordinate generation, similarity, and reaction handling. Use when custom sanitization,

Drives the Rowan cloud quantum-chemistry platform via its Python API for computational chemistry — pKa prediction, geometry optimization, conformer searching, molecular property calculations, protein-ligand docking (AutoDock Vina), and AI protein cofolding (Chai-1, Boltz-1/2), wi

Builds PyTorch-native graph neural networks with TorchDrug for molecules and proteins, exposing custom GNN architectures, task/dataset abstractions, molecular generation, retrosynthesis planning, and knowledge-graph reasoning. Use when a project specifically needs TorchDrug's dat

Generates professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings — biomarker-stratified patient cohort analyses with outcomes and evidence-based treatment recommendation reports with decision algorithms, supporting GRADE evidence

Prepares ISO 13485 certification documentation for medical device Quality Management Systems (QMS) — gap analysis of existing documentation, Quality Manuals, required procedures and work instructions, and Medical Device Files. Use for ISO 13485 QMS documentation, conducting a doc

Processes and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when

Reads, writes, and manipulates DICOM (Digital Imaging and Communications in Medicine) medical imaging files with the pydicom Python library. Use when reading/writing/modifying DICOM data, extracting pixel data from CT, MRI, X-ray, or ultrasound images, anonymizing DICOM files, wo

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

Periodic multi-reviewer sweep of the whole codebase — surfaces a triaged checkpoint report.

Sanctioned lane for non-behavioral work — docs-only edits, dependency bumps, reverts. Type-scaled gates; no TDD demanded of prose.

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Show the codeArbiter command catalog — the public command list and what each routes to.

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Stop everything and surface a rule conflict — persona vs. docs vs. code. Present both sides and the conflict-hierarchy level; the user resolves. No silent reconciliation.

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Verify the active host install, package, command ownership, enforcement{{IF:pi}}, wrapper self-test, and active-dispatch coverage gap{{ELSE}}, and harmless live-fire probe{{END}}. Read-only.

Start a feature: brainstorm a spec, get it approved, then drive it test-first through the pipeline. The one entry to implementation.

Fix a confirmed bug: a failing regression test first, then a minimal fix, then the rest of the tdd gates.

Opt this repo into codeArbiter — scaffold the root-level .codearbiter/ state store.

Read-only 3-metric governance glance — override rate, small-lane rate, sprint low-confidence ratio — each with a trend arrow vs. the prior 20-commit window.

Sanctioned, logged bypass of a gate or hard rule — one audit line, then proceed.

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Zero-onboarding, read-only dry-run of the reviewer fleet against the current uncommitted diff. Predicts reviewers, runs the state-free secret scan, writes nothing.

Trim transcript clutter to extend session lifetime — analyze, prune a copy, or toggle the after-each-turn service. Dry-run by default; gains land at resume/compaction, not the current turn.

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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.