LLM Mart Basic

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

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

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.

Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.

Execute the implementation plan by processing and executing all tasks defined in tasks.md

Execute the implementation planning workflow using the plan template to generate design artifacts.

Create or update the feature specification from a natural language feature description.

Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.

Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts.

Cancel active execution loop and cleanup state

Start task execution loop

Smart entry point for new features with auto ID and branch management

Show current feature status and progress

Switch active feature

Cancel active execution safely and optionally remove the spec

Generate technical design from requirements

Submit feedback or report an issue for Ralph Specum plugin.

Show help for Ralph Specum plugin commands and workflow.

Start task execution loop

Index codebase components and external resources into searchable specs

Create new spec and start research phase

Run or resume an optional prototype

Update spec files methodically after execution (requirements -> design -> tasks)

Open-source super AI assistant & Agent Harness. Plans tasks, runs tools and skills, self-evolves with memory and knowledge. Multi-model, multi-channel. Lightwei…

Open-source AI browser agent for web automation: a web browsing agent and computer-use agent in plain English. Browser MCP for Claude Code and Gemini CLI.

Agent-native trading terminal built on DeepSeek Harness. Crypto, US, CN and HK in one three-column GUI, 19+ hot-swappable connectors, dry-run by default with hu…

Open-source desktop and web coding agent with a first-party host and harness, durable sessions, model connections, streaming chat, and workspace tools.

OrcaReplay — Time travel for AI agents. Record, replay, fork, and debug any agent run with any model. Built by the OrcaRouter.ai team.

A complete toolkit for connecting R and LLMs

OpenSRE — the memory-first AI SRE. Self-hosted incident investigation with episodic memory, knowledge graph, web console, Slack & Teams. opensre.in

A desktop AI coding assistant that works with your local projects. Ally helps you understand code, edit files, search a workspace, manage tasks, and complete de…

【在线免费使用】 简单快速将SQL或DBML转换为美观的ER图（支持 Agent Skill）/ The best SQL to ER Diagram converter (Support Agent Skill).

Operation-bound protection for autonomous AI agents: contain and verify operations before committing changes, understand intent and risk across long-running wor…

Local-first AI coding agent desktop: Electron + Rust host core + pi Agent Harness + user-installable plugins

Local-only Go static analysis engine with a built-in MCP server. Gives AI coding agents deterministic structural awareness: call graphs, impact analysis, symbol…

Self-hosted AI agent workspace with tool calling, MCP, multi-model routing, sandboxed execution, multi-agent workflows, and LLM-authored 3D character animation…

Automated TDD enforcement for Claude Code

High-performance platform for building websites, e-commerce, and web applications—with Native AI, JavaScript development, and a marketplace for portable sites a…

Autonomous AI-agent orchestration engine for job discovery with decision traces, tool adapters, and production-grade run control.

Token efficient Claude Code full Python rebuild. AI Coding Agent in 310K LoC Python.

OPC — One Person Company. A full team in a single Claude Code skill. Adaptive agent orchestrator with 21 built-in roles, 6 flow templates, and adversarial quali…

Open-source, secure environment with real-world tools for enterprise-grade agents.

MCP server for AI-powered GitHub project management — agent orchestration, PRD-to-issues pipeline, sprint planning, and multi-agent swarm coordination