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

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.

`crabbox attach` follows the recorded events of an active coordinator run and

`crabbox azure` groups Azure provider setup commands. It currently has a single

`crabbox bench` records and reports local benchmark timing observations. It is a

`crabbox cache` inspects, purges, or warms package and build caches on a

`crabbox capsule` captures, replays, and tracks lightweight failure capsules.

Save the state of a lease, then restore it onto another box or fork it into a

`crabbox claims list` prints the lease claims stored on the current machine. It

`crabbox cleanup` sweeps direct-provider machines and local provider state that

`crabbox code` bridges a Linux lease's `code-server` workspace into the

`crabbox config` inspects and updates user configuration. It has three

`crabbox connect` resolves a lease and opens an interactive SSH session to it.

`crabbox cp` copies files or directories between the host and a Crabbox-owned

`crabbox desktop` drives a visible desktop session on a lease that was warmed

`crabbox doctor` runs a preflight before you commit to a long workflow. It is

`crabbox egress` gives a lease mediated outbound network: a lease-local browser

`crabbox events` prints the broker's event log for a recorded run.

`crabbox heartbeat` refreshes the idle deadline for one owned lease and prints

`crabbox history` lists recorded remote command runs from the broker. Each run is

`crabbox image` holds the trusted-operator controls for provider base images:

`crabbox init` onboards the current repository: it writes the minimal config

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