LLM Mart Basic

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted struc

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handl

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regu

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BL

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quic

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mo

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand,

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running populat

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when p

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phen

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/p

Run ESM protein language models — ESMC for embeddings and representations, ESMFold2 for structure prediction, and ESM3 for generative multimodal protein design across sequence, structure, and function — locally or through the hosted Biohub Platform API (formerly Forge). Use when

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting t

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting chan

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preproces

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or

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.

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.

SMARTS arbitration — reconcile architectural artifacts against the scaffold and prior decisions; every variance resolved by an explicit, user-attributed choice.

Restructure code with behavioral parity proven through unmodified pre-existing tests, then refactor. No behavior change.

Cut a release the only sanctioned way — derive the target's declared version policy from the commit log, roll its changelog, compose an annotated tag, and optionally publish its exact declared assets. Takes the declared target's name as its only argument, or --dry-run to preview one with no write. The only path to a version tag.

Review a diff with the reviewer fleet, funneled to one triaged verdict. Targets the current working diff, a path, or an inbound GitHub PR.

Exploratory spike on a throwaway branch — answer a named question with disposable code. Never merges; exits to a findings note or {{CMD:feature}}.

Autonomous sprint — one interactive spec gate, then plan-to-PR execution with every auto-decision SMARTS-scored and logged. Hard gates remain true stops.

Daily repo hygiene — review the day's repo state, then perform the cleanups under per-action confirmation. Fast-forward only, never destructive without a yes.

Show the project's current state at a glance — stage, open tasks, open questions, overrides since the last checkpoint, current branch. Read-only.

Wire codeArbiter's statusline into ~/.claude/settings.json, or remove it.

The sanctioned task-board mutator — add a queued task, start one (flips to in-progress and stamps the date, minting a dotted ID on pick-up), or mark an in-progress task done. The only blessed write to open-tasks.md.

Opt-in lightweight STRIDE pass for a sensitive feature before implementation. Not a routine gate — invoke it when a change warrants security thought.

Deep, rarely-convened whole-codebase audit — eleven specialist lenses, a resumable on-disk audit log, findings filed as GitHub issues on approval. Expensive; estimates cost and STOPs before running. Never a required gate.

Watch a PR's CI to completion — diagnose on red, notify and offer the merge on green. Never auto-merges.

Copy a file OUT of a running sandbox box to the host — host-initiated egress only (docker cp). The reverse, a host→container bind, is impossible by construction.

Tear down a sandbox box — remove its container and named volume. --keep-volume leaves the volume; with no id, prune reclaims any leaked ca.sandbox=1-labeled object. Cached images are retained.

Run a single command inside a running sandbox box and capture a JSON result — exitCode, separate stdout/stderr, and a truncated flag past the byte cap. The scriptable exec seam.

Open an interactive shell inside a running sandbox box at /work/repo. Read-only root, non-root user, no host-FS access — explore the untrusted code interactively, then exit.

Pull an untrusted repo into an ephemeral, host-FS-isolated Docker container — clone into a named volume, build a dep-cached image, run under structural isolation. Network defaults to offline. Requires Docker and nixpacks.

Vet a new or changed third-party dependency for license, provenance, and supply-chain risk before any install runs.

Report the health of Architecture Decision Records — aged, unchallenged, supersession candidates, unresolved CONFIRM-NN. Read-only.

Ultra-lightweight, open-source, self-hosted personal AI agent framework in Python with WebUI, tools, memory, MCP, multi-agent workflows, automation, and chat ap…

Governance framework for AI coding agents. It runs them through a five-step workflow (plan, build, review, test, ship) where no step counts as done without evid…

Ultimate Multi-Agent OS for Autonomous AI NPCs 2026

Personal AI Agent Hub 2026 — Build Your 24/7 Autonomous Assistant

Proven 2026 Multi-Agent AI Review System – Verdict-Driven Quality Control

Slash API Batch: Cut AI Costs by 50% in 2026

Web dashboard for Hermes Agent — multi-platform AI chat, session management, scheduled jobs, usage analytics

Agent Skills for Solopreneurs

AirLLM dramatically reduces inference memory usage, letting 70B large language models run on a single 4GB GPU card

Zero, your trustworthy AI teammate for real work.

一套 DSH runtime，Desktop、Web 与 TUI 三种开发体验。

Open-source operational advisor for ClickHouse — real-time monitoring plus AI-driven index/partition/materialized-view recommendations.

⚙️ TypeScript Style Guide and Agent Skill. A concise set of conventions and best practices for consistent, maintainable code.

Framework for AI agents to build and maintain a digital brain through Obsidian wiki

Apache Maka (Incubating) is a local-first AI agent workspace. Model messages, tool calls, tool results, permission decisions, and termination events are recorde…

Neo.mjs is a self-evolving software organism: a professional end-to-end AI engineering team whose cross-model swarm inhabits live apps via Neural Link, Active H…

Agentic development harness for Claude Code — SPEC-driven plan/run/sync, TRUST 5 quality gates, model+effort routing, and Claude×GLM multi-LLM cost control. Sin…

NocoBase is an open-source AI + no-code platform for building business systems fast. Instead of generating everything from scratch, AI works on top of productio…

An open-source AI coding agent that lives in your terminal.

PawWork — free, open-source desktop AI agent for macOS and Windows. Alternative to Codex App and Claude Cowork. BYOK with 75+ providers, ChatGPT OAuth, local mo…