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.

This is the lane for changes with no behavior to test-drive — prose edits, a version bump on an

Use this after a pull request has merged but your local checkout is still on the topic branch.

Prints the public command catalog straight from `COMMANDS.md` — the plugin's own single source

This is the single entry point for turning staged work into a commit — nothing in codeArbiter

The protocol for a rule conflict — not a skill route, an orchestrator-level halt. When two sources

An optional, on-demand drift audit for the bypass case: a merge, a direct push, or a manual edit

This is the populator for a project that already has code to read. Instead of interviewing you about

`/ca:debug` investigates an unexplained symptom and returns a cited diagnosis or a bounded

This is the populator for a project that has no code yet to read. Rather than guessing at

Proves the install is actually enforcing, rather than just present. codeArbiter's worst failure

This is the standard entry point for new work with a human in the loop at every step. A short

This is the entry point for an authorized repair of a confirmed code defect. Give the observed

This is how a repository opts into codeArbiter for the first time. It writes the root-level state

A bare-numbers governance glance — three metrics, each with a trend arrow against the prior

The sanctioned, logged escape hatch. A routine gate — a lint rule, a style check, a non-security

Explicit PR entry and a direct request to open a PR use the same branch-finishing owner.

A zero-onboarding, read-only dry-run of the reviewer fleet against whatever is currently

This is a Feature Forge preview command — the after-each-turn service ships **off** by default and

Compares architectural records with the scaffold and prior decisions using SMARTS.

This is the lane for moving or reshaping code without changing what it does — a rename, an extract,

PiG (Pi in Go) is a faithful Go port of upstream Pi, the TypeScript codebase behind the Pi coding agent. It is a parity-bound translation, not a rewrite: upstre…

An AI Agent that lives in your pocket. Local-first and privacy focused.

Unofficial skill that teaches coding agents to build with TypeSafe AI's Jev: typed decisions, calibrated confidence, and prior art from 150+ community projects.

Adaptive Test-time Learning and Autonomous Specialization

Prediction-market trading engine — Wang Transform pricing on 291K+ contracts; paper-traded across Kalshi · Polymarket · Solana DFlow (Jito bundles) · 633 tests

Knowledge Management for Humans and Agents

Open-source Claude Cowork / Codex / WorkBuddy alternative — a local-first AI office agent that turns one request into real PPTX, DOCX, XLSX and HTML files. Runs…

DeepAgent Code: AI coding agent with persistent memory and control plane

Awesome Jev — evidence-graded index of TypeSafe System One: SDKs, MCP tools, agents, apps and open models. 20 languages, rebuilt every 2 hours.

CLI for Telegram — agent-friendly, daemon-based, with webhook event push.

AI deep-research agent that turns any question into a cited report: plans searches, reads real sources, verifies evidence. Self-hosted, multi-provider, Docker-r…

Event-stream AI Agent framework for building your persona bot 🍊

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…

Local Emperor-style AI agent with Vue WebUI, multi-provider LLMs, streaming chat, tools, skills, memory, and token telemetry.

Open-source AI reverse-engineering agent platform and MCP server for Ghidra, Frida, x64dbg and Rizin — automated PE/APK/binary analysis, CTF and malware researc…

"Never send a human to do a machine's job" - Open Source AI hacking agent

Prismer Cloud

My Personal Blog (Robotics)

Tau Coding Agent - like Pi, but twice as much

Open-source alternative to OpenAI Dots: self-hosted AI chat, tools, approvals, connectors, and computer tasks.