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

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.

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.

Turn a GAIA workflow misfire into a redacted, classified, filing-ready bug report in one read-only pass. Self-diagnoses config issues inline; files probable bugs upstream on confirmation.

Judge-the-form, human-gated hardening. Reviews recurring code-audit-frontend findings and, with approval, drafts the lowest-context-weight form (deterministic check / skill / path-scoped prose rule) into the working tree. Pass `list` to see live candidates or `why <finding_class>` to explain one.

Initialize a new project from the GAIA React template, renames, strips GAIA branding, configures i18n, installs Claude skills/plugins.

Plan a complex feature using GAIA's task-orchestration pattern, structures the work into fresh-context subagent phases for your approval. Does not implement.

Cut a new GAIA release, bump version, graduate CHANGELOG, regenerate manifest, open release PR, then tag on merge. Maintainer-only.

Detect and, on explicit consent, additively append the languages Serena is not indexing to the `languages:` list in `.serena/project.yml`, then prompt a Serena restart. Never mutates without a yes; inert without Serena.

Author an immutable SPEC artifact through Socratic discovery (spec-kit wrapper), then STOP. Terminal, never runs /gaia-plan; it prints a /gaia-plan prompt the human pastes into a fresh session. Pass `auto <description>` for non-interactive mode that answers its own questions.

Maintainer-only autonomous health audit + auto-heal loop. Runs N=3 fresh-team audit-fix-audit cycles with circuit breakers, reports an F-to-A+ verdict (folding in the shared Claude-integration fitness grade) or escalates.

Single post-init onboarding command; detects situation, runs only owed phases; safe to re-run. --reconfigure rotates token and re-selects tools.

GAIA before_specify hook: constitution placeholder check + spec-kit version-pin drift detection.

GAIA after_specify hook: immutability lint over the just-written SPEC artifact.

Close a plan after implementation+merge. Offers wiki-promote for the plan's consolidated SUMMARY.md, cold-consolidates an out-of-band merge, then early-reaps the local plan folder once cost is represented in cost.jsonl.

GAIA self-review: pre-gate-2 review pass on the in-progress SPEC draft.

Close a SPEC after implementation+merge. Optional drain of deferred wiki-promote, cold-consolidates an out-of-band merge into SUMMARY.md, then early-reaps the local SPEC folder once cost is represented in cost.jsonl.

GAIA Socratic discovery wrapper: /speckit-specify for the initial draft, then GAIA's own Socratic clarify loop.

GAIA before_implement hook: render PO-authored UATs into Playwright e2e specs at .playwright/e2e/spec-NNN/.

Promote merged SPEC or plan content into the GAIA wiki.

This project uses the GAIA preset. Bare `/speckit-clarify` is not the clarify path here: core clarify writes an off-shape artifact (a `## Clarifications` / `### Session` block with five-word answers) and carries a question cap GAIA does not use. Run `/gaia-spec` instead — it driv

GAIA-wrapped /speckit-specify: writes through core, then relocates the artifact to .gaia/local/specs/SPEC-NNN/SPEC.md and stamps GAIA frontmatter.

Show or configure the compact Fallow Impact statusline in Claude Code

The fastest way to put Volcengine Ark in your terminal and your AI agent — go from prompt to generated media, multimodal answer, or deployed endpoint in a sin…

本地私有、开源的自进化跨平台 AI 内容发现 Agent：先理解你，再主动从 B站、小红书、抖音、YouTube、X、知乎、Reddit、微博等平台与开放 Web 寻找内容。（支持 deepseek harness 插件） | Local-first open-source cross-platform AI cont…

Persistent memory for AI coding agents — one verified kb_search replaces the grep/find/ls orientation loop. Cross-repo, CPU-only, zero token spend.

AI 时代的伯克希尔：基于 Claude Code / Codex 的价值投资研究框架。巴菲特·芒格·段永平·李录四大师方法论 + 多Agent并行研究。| AI-era Berkshire: a value investing research framework built for Claude Code / Co…

The batteries-included, No-Code FinOps automation platform, with the AI you trust.

Open-source 3D AI agent framework — GLB/glTF avatars with LLM brains, memory, emotions, and autonomous payments. MCP server · x402 · Solana/EVM · Three.js. Embe…

XLSX parser for LLMs, RAG, LangChain, LangGraph, CrewAI, Claude, MCP — turns Excel (.xlsx) into citation-ready JSON with formulas, charts, dependency graphs, an…

Hermes-Relay — Your Hermes AI agent, in your pocket — chat, voice, and control.

A minimalist, terminal-native coding agent written in C.

AI-powered OSINT agent with interactive REPL, MCP server, and CLI. 19 tools. Works with Claude, GPT-4, or local models. For authorized security research only.

AI pair programming in your terminal — one static binary, sub-ms startup, any model

Where data access meets operational intelligence

Build your own security agents. Open-source framework for agents with live, read-only access to your infrastructure, with no path to widen it. Reasons across AW…

Multi-workspace terminal aggregator with Claude Code AI integration

Go implementation of AI coding agent

Harness engineering beginner tutorial, from 0 to 1

Generate images directly in DeepSeek Harness chats

A smarter, self-hosted AI assistant — multi-user, multi-agent.

Turn any research paper into a commercialization report — 6 AI agents, TRL/MRL scoring, patent landscape, market intelligence, verified citations. DeepSeek / Op…

Power BI CLI - semantic models (.NET TOM) and PBIR reports for token-efficient AI agent usage, built for Claude Code