LLM Mart Basic

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

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

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.

Record the present state by mode — decision (ADR, RFC, rule), code (spec, doc, guide, scenario), or research (a ready report or one external material); a gate picks the document type.

First-time Archcore setup — wire host configs, measure the authored context, compose the full first-day seed in one preview, and create it on one confirm; import converts CLAUDE.md, AGENTS.md, rule files, ADRs, and docs into native documents; refresh adds new facts or drills into one domain.

Plan a feature or initiative through a computed route — a small fix exits with no documents, one capability gets a spec and a plan, a large initiative gets an umbrella PRD with one spec per capability; start with sdd, sources (market research), iso (regulated work), or research (technical investigation) to run that path directly.

Review branch changes against Archcore docs, or report project health; drift runs staleness detection, deep a full documentation audit, closeout closes a finished feature, experience captures a repeated pattern.

Verify that citations actually exist and that the claims they support are faithful to the cited source. Runs deterministic existence checks (Crossref / OpenAlex / Semantic Scholar / arXiv) plus a claim-faithfulness pass via the alterlab-citation-verifier skill.

Run a systematic, reproducible literature review on a topic and return an APA 7.0 annotated bibliography with a documented search strategy. Invokes the alterlab-deep-research pipeline in lit-review mode.

Run a full multi-perspective peer review of a manuscript, simulating an Editor-in-Chief plus three peer reviewers and a Devil's Advocate, and produce a structured editorial decision and revision roadmap. Invokes the alterlab-paper-reviewer skill.

Orchestrate the end-to-end academic research-to-publication workflow (research, write, integrity check, review, revise, re-review, finalize) with mandatory integrity gates and two-stage peer review. Invokes the alterlab-research-pipeline orchestrator.

Audit infra security: secrets, deps, CI/CD, webhooks, AI/skill files

Audit Solana program code for exploitable bugs and write a findings report

Compare per-instruction CU with the stored baseline to catch regressions

Build the web client (Next.js, Vite, React) and check env, types and bundle

Build Solana programs (Anchor, Pinocchio, native), incl. verifiable builds

Build the Unity project in batchmode for WebGL, desktop, Android or PSG1

Turn a solana-ai-kit fork into a project: set up CLAUDE.md, remove kit files

Un-ignore and commit the kit config dir, instruction file, .mcp.json and .gitmodules

Replay a user's failing transaction on forked state and map the error to source

Deploy a program to devnet, or to mainnet after the user's explicit go-ahead

Review the branch diff for Solana security issues, CU waste and AI slop

Read-only check of toolchain and kit config, with one fix-it command per failure

Conduit — native SwiftUI iOS client for Hermes Agent

一个现代化的可视化规则引擎平台，用于编排复杂的 AI 工作流。在无限画布上设计、测试和部署 AI 流程——无需编写代码。结合 flowgram.ai 的能力与 Java 服务端，提供生产级工作流管理。在此之上提供AI Agent / Copilot的助手编排能力。

Job application tracker and AI-powered job search assistant. Helps job seekers manage their search journey with AI resume review, job matching, task logging, an…

📝 Markdown and HTML renderer for Svelte 5 — built for streaming AI agent output from Claude Code, ChatGPT, and agentic workflows. XSS-safe defaults, token cach…

ServiceNow MCP server: 500+ tools and 26 AI capabilities for any AI (Claude, ChatGPT, Gemini, Cursor, Copilot). Multi-transport (stdio, SSE, HTTP), A2A, dynamic…

Free crypto news API - real-time aggregator for Bitcoin, Ethereum, DeFi, Solana & altcoins. No API key required. RSS/Atom feeds, JSON REST API, historical archi…

Build production-ready AI agents in both Python and Typescript.

From agent user to agent builder: build a Claude Code-style coding agent from scratch in Python: 8 articles, 4 videos, one codebase

🪁 A lightweight, modern Kubernetes dashboard that unifies multi-cluster and resource management, enterprise-grade user governance (OAuth, RBAC, and audit logs)…

Stateful runtime management for LLM agents—inject, manipulate, and retrieve Python objects across turns.

AgentCall lets AI Agents join meetings with voice, video & screen-share to build together. Supports Google Meet, Teams, Zoom (Beta)

Kition brings Markdown, DataTable, WhiteBoard, a tool-using AI agent, browser research, and visual workflows into one desktop workspace.

IntentKit is an open-source, self-hosted cloud agent cluster that manages a collaborative team of AI agents for you.

A powerful Model Context Protocol (MCP) server providing comprehensive Google Maps API integration with LLM processing capabilities.

Turn your Claude Pro/Max subscription into an OpenAI-compatible API for your IDEs and devices — LAN auth, per-key quotas, response cache, disciplined cli.js ali…

Paw Work - selection-first web agent for Chrome: select on the live page, describe the outcome, take away an editable office file. BYOK, sandboxed, no server.

基于 AI Agent + MCP 工具链 + 渗透 Skill 编排， 配合大语言模型， 自然语言输入 → 自动完成「信息收集 → 漏洞发现 → 漏洞利用 → 报告生成」全流程。

Lexora — Personal AI workspace built around Desktop / 以 Desktop 为核心的个人 AI 工作台

First AI Journey for DevOps - with comprehensive learning paths, practical tips, and enterprise guidelines

AI coding agent with one Python core and three front-ends — headless CLI, Textual TUI, and an Electron desktop. Works with any OpenAI-compatible API, with risk-…